First, I leave the organization more or less to my five year old. That sounds mean, perhaps, but I can only tell him "put the little pieces and people pieces--any special pieces--in the smalls container" (for unique pieces) so many times before my head explodes. And I am tired of being implored to find wee tiny Darth Vader or R2D2, so that's another good reason to get him used to being responsible for it.
I do help him by having a blanket that he can put on the floor for easy cleanup. (Help him fold it up on the corners, then dump into a bin.) We do have a few specific sets, which I did originally put aside separately and explain to him the reason for doing so. He mixed them in.
You can have a special shelf for creations, and then just remind them to put their creations there. I think there's a logical consequence in them learning that if they don't put their toys in a safe place, they get bumped and fall apart. If they get mixed in--" wow, I guess you'll have to look for that one".
You can encourage them to get out one set at a time and keep them in separate the ziplock bags. In my son's room, I actually cleared off his toy shelves because I was fed up with the creations everywhere (and an unwillingness to pick up on his part) so now he has a place to store his creations. The stored toys come out one at a time, so clean-up is guaranteed to happen.
Like Jenny O-- no wonder solutions, this is just what works for us.:) Legos *can* take over.