Preventing Double Payment Instances

We're currently experiencing prepayments resulting at times in double payments. After researching into it a bit, seems there are multiple built-in applications and reports that have prepayment functionality built in.

The three ideas I had to eliminate double payment are as follows:

1.) Use a column in P0411|ZJDE0001 add a payment status code of prepayment on inquiry screen. A/P will see this on initial inquiry screen.

2.) Use P0411|ZJDE0009 / P0411|RIS0009 in lieu of P0411|ZJDE0001 this version has an already existing prepay checkbox
3.) Begin utilizing the already existing applications for prepayment processing P004201 and P0411P

Question is, is it possible to link the prepayment entry to the purchase order to warn finance prior to them entering in the final payment, that there has been a prepayment made?