I just discovered that when you are in the "Receive Payment" window were your overpayment is recorded, you can click on the "Print" arrow and it gives you the option to print credit.  Unfortunately it does not allow you to describe why the reason of this credit to the customer but I think you could fill out by hand the reason for this or you can attached documentation for your customer that will support this credit and let them know this is due to an overpayment.