Im having a little trouble visualizing BUT it sounds like i would use Multi-body parts rather than an assembly. You can turn a multibody part into an assembly pretty easy and this would keep everything in that single design table. I think there is a way but you want to avoid making all these references between files if possible.
DriveWorksXpress might be another option for you.
Here is a list of all the presentations from this past Solidworks World.
Look for Master Model for everyone Chris Castle. He talks about master modeling and how to save out bodies and so on.