I am just now working on this problem and have come up with this idea.
I have a bed liner with slots for 2x4's at about half level. I will rip a 2x4 and come up with two 2x2's.
I'll run these accross the bed both front & rear in these slots. I will screw a sheet of 3/8" plywood to the top and paint all of the above.
This will give me a space under the plywood about 12" tall that is protected from the wind and rain. This will allow me to slide my Rapture 40 under without removing the wing.
This will give me room to store chairs, cooler and pop-up on top as well as keep the plane secure while out of the truck like in the partking lot of a store.
Mark