I travel, and do a lot of kayak fishing along the coast. I do not have a truck shell over by bed. As for getting the kayak on your roof, simply lift the bow of the kayak up and rest it on the rear edge of the shell, lift the back of the kayak, and push it up onto your rack (use a towel to protect the finish on your cab). This also works for those of you who don't have a bed cap if, you just put the bow of the kayak in the bed and push it up on to the roof rack.
My kayak has a rod pod that allows me to store my rods inside the hull. But i'm also trying to figure out a good way to carry them when I don't have my kayak. I'm going to figure out a way to use pvc pipe and have some sort of expansion at the end to accommodate the reels. I want it covered and secure.
When I car camp, i set one of these up in my truck bed, but as you can see, it's easily mounted to the roof as well.