Tom, I'm not quite sure what type of boat you are going to carry, my experience is with 9' to 12' kayaks that weigh about 40 lbs each. I have a system that will carry up to 5 loaded on their sides. I have used this system on two different trucks, both with fiberglass camper shells. I have used both Yakima and Thule (both found in bike stores). I place one load bar on the vehicle cab roof and one near the front of the shell. Consideration must be made to the type of mounting hardware for the placement of the towers and load bars on the shell. I believe the front load bar should be placed on the cab of the truck to provide strength for highway speed and the resulting stresses from 'wind'. I have numerous opinions on both manufacturer's adv/disadv.
Some folks I've seen at the river also use a ladder rack type system. It is custom made to place the load on the bedrails, but provide clearance to slide the camper shell in. These are great, but not removable.
E-mail me if you want more info...
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99 2500 QC 4x4 5 spd 3:54 stock