I have a trac rac i use, but that wont work with your cover. I dont know what else to tell you, other than maybe pick up a utility trailer for the same price as higher end racks. you can get a decent one on craigslist for like 500. other than that... I dunno

 

I usually only carry my canoe when I go camping and I almost always take my Grand Cherokee when I go camping, so it's a simple luggage rack thing.

I have a buddy though who has one of those bed extenders who uses it for his kayak. I've borrowed it a couple of times and it really does work well. I think he give all of $79 for it at a local auto parts store.