Forum Post: Prepayments double counting?

I recently discovered that you can enter pre-payments from customers through Manual Check and Payment Entry.  But, when we create the invoice, using the same number as the PrePayment, it looks like it is double counting it and the customer looks as though they are owed a credit.    I am entering it in the Sales Order Totals tab, as well as the manual check and payment entry.  Could this be causing the double credit? Any ideas on what is happening and now, more importantly, how to remove one of the PrePayments from the customer's account after the invoice has been generated? Thanks so much!