You can build a rack in the back even with the roof line, metal or wood. The canoe is supported on the rack and on the roof. You need a roof rack for the cab roof or a low cost way is to use foam blocks under the gunnels of the canoe.
Another, maybe better way, if you have a hitch, is to build a "T" coming up from the hitch. A piece of pipe with a bolt to go through the hitch that will tighten down and support the top bar. If you rig it so the top bar will turn, it really help when you unload the canoe.
TIE DOWNS
When you tie down you are fighting lateral movement. You can run two ropes to the front of the truck and tie down that way. I prefer to take flat webbing, sew a 'D' ring on both end and bolt it to a fender bolt under the hood. You leave it on permantly. These are fed up and ropes can be tied to the sides. That way you do not have obstucted vision and it holds better.
The front needs two ropes or rachets, ropes at the racks, and I always tie down the the back also. You are trying to stop shifting. Sounds like a lot, but I can tie up a canoe in ten minutes.
Real important for you sanity---- If you are useing the flat webbing like with the rachet tie downs you have to put twist in them. If they are not twisted the will make a very high pitch sound that will drive you bats.
DO NOT TIE DIECTLY TO A FACTORY ROOF RACK!! For coushioning you can use the grey pipe insulation works well. If I tie to a roof rack on a SUV ot a goober mobil, I run ropes through the windows and through the interior. DO NOT depend on a factory rack to take the stress.
I will put in a coupla links to show what I an trying to say.
Good ideas here
http://www.canoegear.com/catalog/home.php?cat=39
Check Thule and Yakima for racks also. I usually get ideas and bild my own.
This is a store at the Bounday Waters Area. Pricey , but good stuff.
http://www.boundarywaterscatalog.com/browse.htm?id=81&step=2
Our canoe in the Boundary Water Canoe Area