In R12 the Intercompany Accounts setup is broken out from GL and included in the Advanced Global Intercompany System (AGIS) product (Don't worry you don't need any additional license for this product). There is a separate set up screen for Intercompany and Intracompany Accounts. The same set up pages are available through the Accounting Set Up Manager as well as AGIS so you can pick your navigation path.
The Intracompany accounts are defined for pairs of Balancing Segment Values (BSV) within the same ledger; this set up is similar to the 11i approach and we upgrade 11i Intercompany accounts to Intracompany accounts here. You don't need to uptake the Legal Entity Configurator product(new in R12) to define these.
In order to enter Intercompany Accounts you need use Legal Entity Configurator to define your Legal Entities and map them to ledgers and/or BSV. You then define accounts to use when certain pairs of Legal Entities trade.
In R12 you can now define a separate payable and receivable account for each Inter/Intracompany trading relationship. In 11i you would just define the due to/due from account and that account was used for both the payables and receivables I had with the specified trading partner.
These will be used for any AGIS transactions you create and also by the automatic intercompany balancing in GL and SLA. Doing the Intercompany balancing at the transaction level in SLA is a big enhancement for R12 and one I will talk about and give examples of in another post.