How to handle a customer overpayment?

I have a customer who paid an invoice twice. I received their second payment and saved it as a credit on the account. Quickbooks doesn't seem to have created a credit memo in connection with that, but when I create a credit memo to send to them, it now says they have twice the credit that they should. How can I create a credit memo from the overpayment without it showing as two credits on their account? In Quickbooks desktop, I was always able to print the credit memo right when I was entering the payment from the customer, but I didn't see that option in Quickbooks online.