I am curious how you will be able to differentiate the different sets when it is time to put it away or will you just combine it and worry about that aspect later if at all?
If I have a box, I actually spend the time to put everything that belongs in the box, back in it. Thanks to Heather's great web site, I can do inventories on boxes when I unpack them and make a list of what's missing so I know what was in the box when we started. When we set up the display, we tried to make it easy to pack away sets by putting the klickies together.
In this case I don't have too many boxes - two boxes for circus romani, the circus ring, the zoo, the hazmat guys, one horse with jugglers set, and one circus truck set.
The other thing I'm trying to do is group like stuff together so finding something takes a lot less time - like fences.