I've found that our canoe seems to fit best in a certain position on the van. If I slide it a bit forward, it doesn't seem to work as well....no real science behind it, but it may have to do with the way the gunnels are resting on the roof rack?
I agree that it won't matter if you're off to one side or the other, as long as you try to keep the keel of the canoe running the same way as the TC....you want the wind to be deflected evenly. Of course, if the canoe is close to center, you can use equal distant ropes to hold it in place, but it shouldn't really matter...especially if you have a special mounting system.
I'd just put the canoe up on top....slide it around until it seems to fit right, and then fasten it down. Not sure if a flag is going to matter, if the canoe is more than 8' in the air....who's going to walk or drive into it? Still, being unsure of the laws, it might be best to put one on.:)
Happy Camping:)
