Defining Accounting Rules for project costing

Our company is working on a configuration to collect costs in Project Costing where the project is associated with a Contract that initiates Billing for intercompany billings.  This is in a PS 9.1 environment. The system let's you define accounting rules associated with the contract that carry through to the Billing module.  But it does not seem to carry them through to AP through the BIGNAP01 process.  That process appears to rely purely on the intercompany template associated with the AP business unit it is sending to with no opportunity to override that at a lower transaction layer, unless we stop the process in Billing to manually intervene and apply a distribution for the interunit expense line.  These billings are for a variety of transaction scenarios each requiring different accouting treatment so that it is not feasible to rely on only the interunit template to set the interunit expense lines for every voucher.  Below are some screen shots of the configuration.

Any creative ideas out there for handling this one?