Jruiz,
I have the 74" bed on my Tundra, with a tonneau on it. If I go somewhere close I'll haul the yak in the bed like you do, but if I have stuff in the bed or it's a longer drive I use my rack setup. The front rack goes across the cab like a standard rack system, and the T-Bar slips into the hitch recepticle. Using this setup, I can carry one/two kayaks and have the bed 100% free for other things. It works for me because you can easily put the system on and take it 100% off the truck. I carry a Cobra Marauder which is for sale, so I don't need the rack system anymore. Both the front and rear racks are Thule.
The rack systems others have spoken about look pretty nice and probably works well for their application. There's many ways to go, that's for sure.
