Hi BAB,
I assume you are entering intercompany transactions in the AP Voucher and Adjustment screen. In that screen, the AP account is usually credited. But there will also be a credit generated and it will usually go to the Due To or Due From account when the intercompany transactions are created. You can see the intercompany entries generated by the system by going into Intialize Mode and looking at the Journal Transaction screen for that AP batch. You cannot see the intercompany transactions in the AP module. Also, the intercompany credits or debits are determined by the setup you have in the Intercompany Account Subaccount screen in the Multi Company module.
Let me know if you have additional questions or if I have misunderstood your question.