Brock,
I am not sure I get all the details in your question, so just refering to the 2nd passage :
you surely can replace top level component (part or subassembly) by its Interchange "buddy". What you need to do is to :
1. add this top level component to Family Table as an item
2. In respective top assembly instance cell in tghe table, go to Tools / Replace BY / Interchange - and browse to the needed interchange component.
3. Your instance of assembly will contain the interchanged comp. now.
Let me know if your intent was for something different.
Regards
- Vlad