Over payments may be for advanced payments, where a customer wants to have a running credit which will be used up when charges like site fees become due.
Just accept the payment as detailed above and when the charges become due, enter them in the charges screen and Store (accrue) the charge using the N key. This will then subtract the charge from the credit balance. Note that no receipt is printed as a receipt for the credit has already been printed.
As confirmation for the client, a statement can be printed.
Note that charges posted through recurring sales will also use up any advanced payments.
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