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.
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.