I have used Chips method of stacking the canoes with the uppermost one hull up, and it works quite well but it does create a lot of air drag and might be a problem if you have to drive under anything low. If you get caught in a heavy rain you might also be taking that top boat off in a downpour.
I would probably try putting the boats on their sides. If the sheerlines are somewhat comparable they might nest together fairly well and most boats are significantly less deep than they are wide.
Kayak & Canoe Covers
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