How to Refund an Overpayment from an Owner/Customer
Enter an AR invoice for the overpayment that hits a clearing account (suspense for example). Apply the cash receipt overpayment to this dummy AR invoice. Then enter an AP invoice to the same clearing account as the AR invoice. At this point the clearing account will zero out. You can then cut a check to the customer/owner out of AP to refund them the overpayment.