Customer paid same invoices on two different checks.

A customer paid multiple invoices on a check.  The check was credited against the outstanding invoices in the customer's account with the funds going into Undeposited Funds account.  A week later, the customer issued another check for multiple invoices, including two invoices that were paid on the check from the week prior. When entering the payment received on the second check, the two invoices did not appear in the customer's outstanding balance. Nevertheless, I credited the check toward the outstanding invoices and entered that payment of the total amount of the check into Undeposited Funds. However, I do not see a credit balance on the customer's account.  How do I correct the entries to show the customer credit as I'm certain the customer will tell me to issue credit toward future invoices?