got any pictures??? post em up and we'll see what we can do.. sounds to me that the canoe wont contact the front of the canopy.. so if you build a little thing (like 2 end pieces and a cross piece) like a 3/4 rectangle type of dealy.. coming off the cap in the front and the same height as the back or even higher, then put a piece on the top of the back so it wont touch the cap and **** it up. now lay your canoe upside down on the top of the truck.. i'll see what i can draw up in "paint" for ya so you get an idea of what im talking about.
here's my sweet paint skills.. not the best picture but you get the idea... oh and i used my truck as an example. if you post a pic of your truck i can murder that one up too!!