Ideally, you should enter your invoices first so that you can apply the payments. If you decide to do this, you will have to use a tool like Pro Transaction Importer. Otherwise, if you can identify which deposits belong to which customers then I would just import the banking transactions, categorize them to the appropriate sales account and customer.
Once you’ve got all of your historical information into QBO; then you should follow this workflow in QuickBooks going forward. I’ve also included a link to the video tutorial that we have on each of these in our QuickBooks Course:
1. Enter Customer Invoices: https://fitsmallbusiness.com/send-an-invoice-through-quickbooks/
2. Apply payments to open invoices:
3. Deposit payments to bank account: