I cannot advise you on this since I just slide my NuCanoe into the back of my Ranger for hauling, but, as I think about your situation, I have a concern that may be thinking too much! Since the cab of the truck is not attached or part of the bed of the truck, I would think you would either want the rack all on the cab or all on the bed. As you travel ruts and bumps, the bed can twist and move when the cab does not and maybe this would create a problem. Trust me, this is just thinking through this and this may not present any problem.
Just thinking out loud and nothing more....
Warren
Fly fishing and fly tying are two things that I do, and when I am doing them, they are the only 2 things I think about. They clear my mind.