The height of the racks should not be a big deal. That said, some considerations are, 1) how easy/difficult will it be to get into the box while loaded? 2) Wind resistance? Canoes can catch a lot LOT of wind. They can be like towing parachutes. The lower the canoes, the lower the wind resistance. Also, think crosswinds. If possible rig so the bow is lower than the stern. Anything that cuts wind saves gas. Don't forget, gas will go back up one day...