I can't really confirm for sure what I am about to type here, but from my experience if it's a rather large assembly with more than just one level then it's better to avoid the use of Session IDs, cause each and every assembly or subassembly uses different IDs for same components.
Imagine year or two later you will have to update the assembly with new parts, and try to restructure some components, you will realize that the assembly is better off without these "part" relations, cause of aditional regen time, and lots of yellow lights.
Putting these relations into post-regen field might be an option if relations worked the way they should. Well, maybe on some older version of Pro/E, just try it by yourself and you will see.
If you want everything to be associative. Your best bet is the Top Down design as mentioned by Tom. That is use of a skeleton model with intent selections in features built on part level.
If I didn't want everything to be associative, I'd use Session IDs such that I'd first apply the relations to each of the parts via the assembly, and then I'd just comment them out, so the parameters would become part-only and the assembly wouldn't be bothered with this link anymore.
This little example may sound too confusing or maybe even too simple on the other hand, but let me try. I haven't used SIDs for a while so I might be all wrong, I just doubt you can "force" the assembly to create parameters on part level. So these would all need to be created upfront in each of the assembly parts. Now what if you add a part into the assembly such that the Session IDs get mixed up on their own. You won't see an error cause the relations window isn't opened anymore, in case the parameter isn't predefined in the newly added part, just like it was when you first defined the whole SID thing.
Well, would the assembly just crash then? I have no idea.
Could it be something that could prevent you from changing the assembly? I guess yeah. Just more and more obstacles to come around.
No matter what way you choose, don't forget to share you experience here. 