Here's a picture of Mike Haverly's rack for his Ranger p'up. On the other hand, some put a sheet of plywood at top of box level, leaving a huge shelf to slide models onto. Chris Cox has his setup this way (Mazda P'up, I think). Paul W. has his wife's Dakota P'up setup this way, too.
Using the shelf method, it would probably be good to have bubblewrap covers for the models, and some method to keep them in location. Maybe pulley and 1/8" nylon line, lashed to cleats on the rear of the shelf. Good thing is that your lower level is left open to heavy stuff, flight boxes, fuel jugs, luggage, ice chest, sunshade, etc.
Then again, the rack might be better for local flying outings. I'm trying to decide, as I got a new '06 Toyota Tacoma (6 speed!) in November. I'm leaning toward the shelf method, and wondering if I can make a 2-layer deal, maybe put the models in racks on the shelf, made from 1/2" or 3/4" PVC pipe.
Steve