When a customer
overpays, Money will keep track of the credit. When you receive a
payment, Money will assign it to any outstanding invoices for the
customer you choose, and record a credit if the payment is more
than the amount owed. If the customer has no outstanding invoices,
Money will tell you that all invoices for that customer are paid in
full and ask if you want to credit the payment to the customer.
In the left pane, under Common tasks, click
Receive payment for invoice.