I just place them in the spots that look to be most vulnerable to getting contacted by the boat, place the boats on, adjust them as needed, then use the pressure of the boats sitting on them to hold them in place. If you are afraid of the funnoodles moving, you can feed a rope through the hole in the center to secure them.
It really works, and it's really cheap. I have bought those kayak carriers before, and figured out I don't like it any better. In your case it's just one boat with a really large cockpit. Most likely the entire cockpit is going to be over the roof of the car. The Canoe kits you can get for about $20 at most sporting goods stores would work great, it comes with 4 pads that fit on the edge of a canoe (Or a kayak cockpit rim), and the straps you need. The funnoodle is cheaper to replace if parts are lost and more versatile, but if this is the only boat you are getting for a while the roof top canoe carrier kits might be a good investment because it is a better option.
For multiple boats I prefer the funnoodle route until you can get some real roof racks.
Here is the canoe carrier:
New kayak owner!
installed:
New kayak owner!
That will work on the cockpit rim of a tandem kayak. And it's maybe $10 more expensive in the long run.
