I put together a „logistics“ box (above left) which contains all the non figure stuff that goes on the table (the score board, the lists, the list markers, etc). This way, I pull things from each box in turn while setting up.  I also put together a „game master“ tub (above right). This has all the stuff I and players use to actually run/play the game (the reference sheets, cards, tracking mats, dice, pencils, clip boards, etc, etc).  

The devil is in the details, of course, with customized storage. You want to not only be able to easily tell which box is which when setting up, but the real challenge with customized storage comes when you try to put things back–particularly under a time constraint. Not only do you need to get the right figure into the right box, but it also has to go to its own spot. To help with this, I put a picture on each box lid, a one-brain-cell solution that anyone can follow (even players who want to help  take the game down). 

Above: the complete game system compartmented into four bankers boxes and one tub, a fairly compact and easily transported configuration for such a large layout. The figures and foam are not heavy, so those boxes are an easy lift. The game master tub has a bit of heft, but is easily managed.  Most of all, when I want to hit the road, all I have to do is load things into their pre-designated spots and go. The only thing not included in the boxes are the three game mats that I put down (one under each list). These are Fat Mats (Grassy Field) that each come with a own carrying case (and sling); so they are equally easy to bring along.  

Some may think this is all a bit „over the top.“ But my experience has been that this kind of work done up front allows me to focus on other things once I’m at the convention. I also generally prefer to run convention games as opposed to playing in them, so I think of this sort of preparation as being as much a part of the hobby as painting figures.