Thanks for joining in this forum, @Designer2009. 

As an additional insight, the system will only record a single Payment transaction with a negative balance rather than two transactions (the credit memo and the payment transaction) (indicating the overpayment). 

This is to prevent duplication and keep the list of transactions for your customers organized.

You can manage the overpayment in a few different ways. Check out this post for further instructions: Handle a customer credit or overpayment in QuickBooks Online. 

Get back to us here at any time if you have additional concerns. Take care!