Re: little toys that come in sets...like barbie or lego
With barbies we toss it all together in a bin. Frankly, I just in the last year stopped picking all the little pieces out and hiding them from the kids (dd1 didn't know barbies came with shoes until she was almost 5). My kids never question mixing the barbie stuff.
Legos I leave up to the kid. Dd1 will often ask to keep the set seperate for a month or so while it is still new. Eventually she will just start dumping them in the bin of legos herself. Her birthday legos she got 2 weeks ago are still seperated but everything else is all ixed together. I predict by Christmas she'll stop keeping those seperate as well.