I had this same issue as our customers pay in increments and deposits and not total invoice amounts. It took me no kidding 3 weeks to get someone competent at quickbooks who had any idea what they were doing or how to fix a problem THEIR system creates because it is basically just dumb. The person I was working with for almost 4 hours finally got to the problem root and told me to do this, hope it helps:

When a payment is received on your banking feed and you have an open invoice>you click on the payment/deposit and click find matches>once there make sure the end date is the last of the month for whatever month you are in> scroll down to match the correct invoice.

From there the invoice is linked automatically to the online bank payment and will update amounts or show paid in the system.

From what I understand the only thing that has to be completed to make it report correctly is the matching of the bank deposit/payment with the invoice. I was told not to categorize anything as that is what creates the duplicate reporting of payments/deposits. We did have to go in and make sure my invoices were setup to show paid in A/R and not the "bank" register for quickbooks but if that is done then your process is just that one step.

I do totally agree with everything everyone is saying about matching. I cannot tell you the amount of time I have spent undoing what quickbooks did and just today spent another 2 hours with their customer services because their "payroll" system is reporting as duplicate payments to 2 different accounts as well as the payroll taxes paid/withheld. Only to be told to make the duplicate account THEY created inactive, which as everyone knows does not work since quickbooks will still log payments there. Don't even get me started on not being able to combine accounts or merge things in the chart of accounts and no delete option. Like who designed this system a 3yo!?!?!?!?