AR/Sales Order - What is the best way to handle processing of prepayment matching to sales orders/in

We are looking for the best way to handle processing of prepayments of orders.  How should we tag the RU entry when creating the un-applied cash (say with an order # or quotation#) and also how to tag the SO (in cases where prepayment is based on some quotation # (assigned of JDE but known at SO entry time) so that it can then later be matched to a Sales Order/Invoice once it has been Sales Updated?  Is there any current method to then process these matches or do we need to create a custom process to load F03B13Z1 for