Make payments to an account without an order (make overpayments that can be kept as a credit for future use)

We sometimes have schools over pay or different people over pay on their account but we still have to enter the full check amount into the system so it goes into Quickbooks properly, but the system wont let me enter a check amount over the total bill. Sometimes we end up refunding the amount and sometimes we end up keeping it as a credit on the account, but I do need to balance the checkbook showing I deposited the $****.** check they gave us, even if it was more than what the invoice shows