I recently got a new ride for my Prangler 14. I bought Thule bars, and a couple of front tow eyes. Together with my old set of Hully Rollers, I was set. Took it out for the first time just yesterday. No problems and having the 'yak up there only cost me one mpg highway in calm conditions.
Side View:
And the Hully Rollers that make loading so easy:
I've never noted any hull deformation after the tie-down straps are removed, but I'm careful to put the cross bars under scupper areas. On my Durango, I made a wooden block that fit into the drive hole - it prevented any side-side movement and also helped with fore-aft sliding. I'll probably add that to this rig soon.