I have been whitewater canoing and kayaking for many years. The front and back lines are never used to secure the boat to the roof. Pull those suckers tight and you'll fold your boat. Now, if you have one of those heavy duty 8000 pound canoes, I don't think it'll be a problem. Whitewater canoes are light enough and flex enough to have issues.
anyway... where I was going with this... We mounted cross beams on the roof rack (one at the front of the roof, one at the tail) with the ropes attached in the center of each crossmember. You center your boat on the crossmembers and push it up against the rope mounts (now it's nice and balanced and straight). Bring your tie-down ropes over the canoe and loop under the crossmember right next to the canoe. Throw a tie-down loop in the rope and pass the loose end through it and pull it down TIGHT. Couple loops around the crossmember and half-hitch it. It's not going anywhere. Now... for security in case your ropes break or your rack comes loose, drop the rear painter to the trailer hitch or other tiedown spot. Take the front painter to the front of the vehicle and tie it off onto the nifty little mount loop that I'lld escribe next. Neither of these ropes should be heavily loaded, just taunt.
Front tie-down...
Get a 6" length of braided nylon strap (or parachute strap) that is thin and about an inch wide. Open your hood and locate a fender bolt near the front of the fender. Remove it and pass the bolt through a washer, the strap ends and bolt it back into the fender. There should easily be enough clearance for the strap. When you need it, pass the strap loop between the fender and the hood and use it to tie to. When not needed, it can hide under the hood.