I looked on your site and didn't see an example. Nice truck/build though.
I think what you're getting at is the oddness of the rail towards the rear of the cubby box. You need to build a little spacer that lifts it up over that rail to fit it. At least that it the way it is with tuffy boxes. You will need a smaller spacer in front to clear the front rail also, but that depends on how long your box is.
Helping at all? didn't think so but I will try to dig up a picture.
Basically lift it up a bit to clear the rails.