First, it's not completely mine. I stole the idea from this guy... http://www.boardgamegeek.com/filepage/112129/imperial-assault-custom-insert
I absolutely loved his design, but me being me, I had to tinker with it and make it my own. I'm in the beginning stages so below is my 1st level.

You see that I like to keep my tiles separated by numbers except the large tiles. Which are separate and resting nicely on top of the other ones in baggies.
In this level I have all the tiles and all the Imperial mini's. I currently have room for the upcoming imperial character packs except for Weiss. I don't know what to to about him. And room for more tiles when they are released.