Paychex is a cloud-based payroll and HR platform that helps businesses manage human resources, benefits, and payroll with its Paychex Flex software. Before signing up for its payroll and HR services, you’ll need to decide whether you’re small enough to use its Paychex Go plan or if a more premium Paychex Flex plan would work better. Paychex Go is a good fit for small businesses with up to 10 employees; Paychex Flex is designed for 10 to 49 employees.
To set up the software, new clients work with an implementation team that imports all of the company’s existing employee and payroll data, making it easy to get started on the platform. Running payroll with Paychex is also simple—just finalize data for a pay period, review the relevant reports, and submit. Paychex handles processing and provides status updates along the way.
How to Set up Paychex Go to Run Payroll
1. Sign up for Paychex Go
If you need to be up and running quickly and don’t need the personal service that comes with the higher Paychex Flex plan tiers, you can sign up for Paychex Go in a matter of minutes. Just go to the Paychex website and review the side-by-side comparisons of each solution. Under Paychex Go, select the button that states, ”Sign up Online.” You’ll have to enter your name and contact information (email, phone number) and wait for a sign-up link that will be sent via email; it usually takes seconds.
2. Choose a Username and Password for Your Paychex Go Account
Once you select the link, you’ll be taken to a page and prompted to choose a username and password. Select “Continue” when you’re done. You’ll see a page with three steps that outline your setup process: Provide business and employee information, Sign documents, Run Payroll. Select “Continue,” and choose whether you’ll be processing payroll for a business or household (i.e., if you’re paying a nanny).
3. Answer a Few Questions About Your Business and Employees
You’ll tell the system whether you’ve paid any employees during the current year; Paychex wants to ensure the year-to-date payroll numbers it provides are accurate. And you’ll be asked how many employees you have.
When your dashboard populates, you should see a green circle with a white check mark in it beside the “About You” section. This means it already transferred over the information you entered about yourself, so you can start entering company information. When you’re done, select “Fix Issues” at the bottom of the screen, and the system will list all of the items you’re responsible for that need attention.
As you progress through each payroll input screen, you’ll notice some information is already in, i.e., an answer to the question, “Have you paid anyone this year?” Other areas will be blank. Correct any inaccurate information, and enter the data as best you can.
Paychex gives you the opportunity to enter employees now or later. If you choose to enter them now, be sure you have basic data, like their names, pay rates, benefit deductions, and so on.
Once you’re prompted to provide your federal employer identification number, you can select the “Verify” button to have Paychex confirm it’s legitimate. This is helpful if you’re relying on memory and don’t have your federal tax ID# handy.
The system also knows whether or not the state you’re in charges income tax. It makes its decision based on the address you enter when signing up for the service.
You’ll then enter the routing and account numbers associated with your bank account. This is where Paychex will withdraw funds to cover your payroll. Then, select “Finish.”
To learn more about Paychex Flex plans, including its PEO option, check out our Paychex Flex review.
How to Set up a Paychex Premium Plan to Run Payroll
1. Request a Quote for a Premium Plan
If you opt for a premium plan, like Paychex Flex Select, you’ll need to select “Get a Quote” under the solution you’re interested in. The company doesn’t publish pricing for its premium plans and, instead, relies on a custom quote process.
You’ll be asked to provide information about your company, including name and size. Then, click “Next” and add personal contact information and whether you’d like to be contacted by text. You can also speak to a member of the sales team by contacting them via phone or email.
Once you provide the necessary information, a sales engineer will contact you regarding your business’ needs; you’ll also be able to schedule a demo to see how the platform works. If you have preliminary questions and aren’t ready for a quote, take advantage of the live chat tool available from the Paychex homepage.
2. Sign up and Work With Your Implementation Team
After being contacted by a Paychex sales rep, you’ll have the opportunity to review the price quote, ask questions, and sign up. You’ll then be assigned to an implementation team that will help you set up your account, including details about your business and human resources team. The implementation team also helps new clients import all of their existing employees, year-to-date payroll data, and any other existing HR information they want to integrate with Paychex.
After processing a few payrolls with Paychex and working with the implementation team, you’ll be transitioned over to a customer support specialist who can provide ongoing assistance. You can view contact information for your specialist in the Assigned Specialist tile on the user dashboard. Users can also reach out to the 24/7 hotline and review the frequently asked questions portion of the Paychex website.
3. Customize User Dashboard and Preferences
If you haven’t already, take some time to customize the user dashboard based on the features you use the most. Because Paychex offers employee benefits management, time and attendance, and hiring and onboarding in addition to payroll, there’s a ton of functionality and it’s important to have easy access to your favorite tools.
Customize your dashboard by clicking on “Manage Tiles” in the upper right portion of the dashboard and select which tools you’d like front and center. You can also arrange tiles in the order that works best for you. Tiles you may want to prioritize as a payroll administrator include Current Payroll, Last Payroll, Tasks, and Analytics & Reports. The Assigned Specialist tile also makes it easy to get in touch for one-on-one support.
To update your user preferences as an administrator, navigate to your profile image in the upper right corner of the screen and make adjustments like changing your profile photo. You can also make changes to company information and settings by clicking on “Company Settings” in the left-hand menu.
4. Assign User Access
In addition to customizing your own administrator dashboard, you can assign user roles to limit what each employee can access and edit within the Paychex ecosystem. This portion of user customization is typically handled during the implementation period but can be updated through the user dashboard at any time.
Access these settings via the “User Access” tab on the left-hand menu. Simply scroll through employees in the user access grid and assign specific roles—like Payroll Admin or Super Admin—to relevant parties.
5. Personalize Reporting and Analytics
As with user preferences, Paychex Flex lets administrators choose which reports and analytic tools they utilize in their HR and payroll operations. Paychex features more than 160 standard dashboards and reports, including totally customizable analytics. There’s also an interactive reporting tool that lets users access helpful insights and on-screen feedback through the online platform.
To choose which reports are generated by Paychex—and view those reports—click on “Analytics & Reports” in the user menu. As with the main dashboard, you’ll be able to choose which tiles you want to view (and the order in which they’re arranged) by selecting “Manage Tiles.” To view all of the available reports, select “View All Reports” from the Quick Reports tile. Administrators can also create sets and favorites once they know which reports they access most frequently.
In addition to standard reports, administrators can customize certain reports by adding or deleting columns, choosing Excel vs PDF, or including specific employee groups or departments.
6. Add New Employees
As new employees join your team, you’ll need to add them to your Paychex database. If you’re using Paychex for hiring and talent management as well as payroll, navigate to the “Hiring” tab in the left-hand menu. You’ll be able to use this Paychex tool to both hire and onboard employees, during which time new employees can add their personal information, direct deposit details, tax information, and other custom information specified by the employer.
Alternatively, you can manually add an employee by clicking on “Add Employee” in the People tile on the user dashboard. Either way, all of the employee data will be updated throughout your business’s entire Paychex database.
If you’re interested in running payroll with other payroll solutions, check out our top payroll service picks.
How to Run Payroll With Paychex Flex
The process for actually running payroll in Paychex is extremely straightforward. Both Paychex Go and Paychex premium plans use the Paychex Flex software.
Follow these steps to run payroll each pay period:
1. Access the Flex Payroll Grid
When it comes time to run payroll with Paychex, the Payroll Center makes it easy to view every employee as well as the total numbers of checks and hours and amounts to be paid. To access the payroll portion of Paychex, click on “Payroll Center” in the left-hand menu. You’ll be directed to a list of active payrolls as identified by check date, company, status, and history.
If you use Paychex for time tracking and attendance, employee data will automatically display in the Payroll Center. However, payroll administrators can also import payroll data from other time management tools by clicking on the down arrow next to the “Begin/Resume” button.
To select a payroll to view, click on “Begin/Resume” and scroll through employees, search by name or ID, and view general data like the numbers of checks and hours worked and the amount of dollars to be paid. Individual payroll administrators can also customize a grid layout that makes the most sense for their needs. Filters also let administrators view specific employee groups like departments or hourly vs salaried employees.
If an administrator needs to review or edit an employee’s profile, they can click on the employee’s name in the grid to access everything from basic personal details to direct deposit and tax information. This portion of the Payroll Center also makes it easy for administrators to view check stubs and reach out to employees with questions or payroll updates.
2. Review Reports and Make Edits
Once you’re happy with all of the data in the payroll grid, click “Review & Submit” in the upper right corner. You’ll be routed to a page where you can view preprocessing reports and other relevant payroll details. This page also lets you choose from quick payment options, including real-time payments, same-day ACH, and standard ACH.
The Preprocessing Reports section of the page includes documents like the Payroll Journal, Cash Requirements, and Job Costing reports in both PDF and Excel. The Payroll Journal shows the complete gross and net pay for each employee, including department and company totals. The Cash Requirement document shows when funds will be withdrawn as well as a comprehensive itemization of funds.
Just below that, you’ll see the Quick Totals section where administrators can view how many checks are going out for the pay period, the total number of hours being paid out (including a count for overtime), and total payment amounts. Administrators can also see if there are any individuals without checks in case they missed somebody.
If you see anything in the reports that you need to change, navigate back to the Flex payroll grid by clicking on “Edit Payroll.” Administrators have the ability to go back and forth between the reports page and the payroll grid as many times as necessary before submitting payroll for processing.
3. Submit Payroll for Processing
After reviewing the relevant payroll reports and confirming that all of the information is correct, click on “Submit Payroll” in the upper right corner of the dashboard. Payroll will then be processed within 15 minutes—though there is a short window during which administrators can continue to edit the payroll information (this can be accessed from the user dashboard).
Once you submit, you’ll receive real-time notifications from Paychex indicating, in the first email, that the file has been processed and, in the second email, that the payroll reports are ready. You can then access reports by navigating to the “Analytics & Reports” tab in the left-hand user menu.
Tips for Using Paychex to Run Payroll
Paychex makes using a payroll platform easy by providing comprehensive setup assistance and customer support. What’s more, the available automations and customizations simplify and streamline the payroll process. Follow these tips to make the most of Paychex for payroll:
- Let the implementation team do the heavy lifting: Unlike some HR and payroll tools, Paychex provides its customers a comprehensive, guided setup process. This means you won’t have to manually add all of your existing employee information or upload year-to-date tax information. Instead, you’ll be assigned to an implementation team that handles setup for you.
- Take advantage of customizations: Not only does Paychex offer users a robust HR, payroll, and talent management platform, it makes it easier to use these tools by providing a customizable dashboard. Make the most of this by personalizing your dashboard in a way that streamlines your most common activities—like reviewing and approving payroll or reviewing analytics and reports.
- Personalize reporting and analytic tools: Users can also optimize Paychex reporting tools by customizing reports and analytics. Once you know what kind of information you need to access most frequently, optimize your reporting dashboard by selecting favorites. Take advantage of additional customization tools by choosing which columns go in reports and how they are formatted.
- Use the CARES Act tools: Paychex now offers support to help businesses navigate the impacts of the Coronavirus Aid, Relief, and Economic Security (CARES) Act. This includes compliance support, HR guidance, cashflow management, and other tools. Businesses can also use Paychex to demystify Paycheck Protection Program forgiveness and tax implications.
For more tutorials on how to run payroll with different software or just access to training programs, check out our guide on how to get the best payroll training.
With Paychex, you can do payroll using Paychex Go or a Paychex Flex premium plan. Both use the Paychex Flex software system, but you can set up Paychex Go within minutes. Paychex Flex premium plans require more lead time—it could be weeks or a month—but you’ll receive personal service and customization throughout the entire process.
Sign up for a free Paychex Flex demo today.
Other articles you may be interested in …