For the tokens, I do this:
The long, skinny rectangle is for environment tokens. Monorail, Mist, Lava, Dinosaurs, etc.
The big rectangle in the middle is for characters and related things; All hero/villains, Citizens, Bots, etc. The next 3 slots in the middle, going in a line starting from the big one, are:
Every-game stuff. Health tokens, Attack/Defense +/- 1, Aim/Dodge, turn order.
Baron Blade Scenario stuff. Turrets and Battalions, basically.
Omnitron/generic scenario stuff. All Drones, Omni-Reaper (sideways next to the rest), pylons/oblivion shards, Exclamation points.
Cards go in the other two, elevated slots. I divided them between heroes and villains/scenario/environment cards, but it doesn't matter.
Map tiles go in the middle; there is kind of a shape cut out for them.
Character Cards go perpendicular to that long, skinny hole, divided into 2 stacks so they cover that whole area.
Then the rulebook, and then the scenario books.