Is there a way to record Order Information on Prepaid Amounts?

For some customers we require that they prepay before an invoice is created.  They reference the order number when they make payment, but they may prepay multiiple orders on the same remittance, or the amount that they prepay may not match the invoice amount.  If we could record the order information on the RU when the payment is made, in some field that would allow matching once the invoice is created, the process would be much easier. Has anyone found a good way of managing prepays?