They now have a roof rack system that lowers the kayak over the side of the vehicle called the Hullavator.(sweet!) They are not cheap. Here's the link for Thule racks.
http://www.thuleracks.com/thule/default.asp The rack is called the . You could also just get foam blocks to attach to your existing roof rack if you have one. I have done it both ways. The foam blocks are ok. But, I would not want to take them too far. I now have a Yakima rack and can fit 2 kayaks on my car.
Good Luck and enjoy...
