Unfortunately I haven’t used Quicken in quite sometime. However, I was able to find a pretty detailed article on how to receive payments from customers and make deposits. It sounds very similar to how it is done in QuickBooks. You must receive the payment against the invoice and then make the deposit. I would just delete the deposits that automatically download because I think recording the deposit right after the payment is the best way to do this.
Here is that article:https://www.quicken.com/support/how-receive-customer-payment-quicken-home-business.
Hope this info helps.
Thank you for reading!