AD Sites and Services

I have four dealerships (separate subnets) linked by MPLS with two different domains in operation (actually two different forests, technically, I guess).  Let's call them A.com and B.com.  Three of the dealerships (previously a separate company) are on domain A.com and one is on B.com.  A.com has a DC in each of its three dealerships with the PDC in the new headquarters building.  B.com has its PDC in its separate building and a backup DC in the main headquarters building where A.com's PDC also resides.  All domain controllers are running Server 2003, but the functional environment is Windows 2000 since A.com's DC's had been running Server 2000.  My question is how to properly set up Sites and Services with this two domain situation.  We have (or had) a two-way trust between A and B, but recently, I am only able to validate that trust from B's PDC to A and A's PDC in the main headquarters building to B.  The DC's in the other two dealerships say they can't find a DC to validate the trust with B.  Under B's Sites and Services, I have two sites created, one for B's backup DC in the main building (with that backup DC as the server for that site) and one for the building the PDC is in, but under A's Sites and Services, I have only one site setup with all three DCs listed as servers for that site.  I do, however, have all four different subnets listed under A's Sites and Services, but only two subnets listed under B's as of right now.  Do I need to create a site under A for B, and vice versa, even though they're on different domains?  Needless to say, I'm a little lost, and this is a long-winded question.  Any help would be appreciated.