@Echo is correct, I did not sleeve my cards. What I have done is set up the box along the following lines:
I oriented the box so the bulk of the wider card slots are on my right, with the long row of narrow slots to my left. At one end of the left hand side is a slot that's a bit wider than the others, that's oriented closest to me. The left hand side fits all the item cards from the basic set plus the item tracker deck (which is a bit wider) at the very bottom of the left side. Then on the right side I keep 4 pre-set 10 card player decks (xenostathem cards plus the militia cards) for ease of pulling from the box. Next I go to the bottom of the right side (closest to me) and insert in the following order: Division Cards, Wave 3, Wave 2, Wave 1, Expansion decks (Grafting and Psychogenics labs), Wave 3 troop stack (including the 2 extra kickstarter exclusive troops), Wave 2 troop stack (including the 2 extra kickstarter exclusive troops), Wave 1 troop stack. This should leave 3 card dividers between the player stacks and the wave 1 troop stack.
Following that my base tracker sits in the slot provided, then I stack the 4 kickstarter lanes 2 high, then place the kickstarter mat over them, and then the rulebook. The cover slides on with about an inch gap from closing all the way.
Hope that helps others figure out how to set-up the box.