How do you handle negative receipts?

We are trying to implement a process to handle a file of ACH and Wire transactions from the bank.  We already have an existing lockbox program set up to handle check payments, and I handle negative receipts there by putting them as Unapplied on a customer's account.  That is happening a custom preprocessor program I created that generates a flat file for Oracle's Lockbox process, and it works great.  Now however I'm trying to use the AR_RECEIPT_API_PUB functionality to apply the ACH and Wire transactions.  I have a case where the customer has sent through an ACH payment for a total of $237k, and wants to