I have 2 of Skookum's pontoons. I used to put them inside my 13 1/2' Columbian when we would go up to Kamploops for a week long fishing trip. I always took them fully assembled but slightly deflated as the elevation difference was enough to really put a strain on the tubes.

One time on the way home we had to stop twice to refill the tubes due to the difference in pressure from the altitude change. I never had any problems with chafing or wear on the tubes. My biggest problem always came from the altitude change deflating/inflating the tubes.

Also, I always used separate cam lock straps to secure the boats. That way it was easy to pull them out and fish. I also used to put the two of them fully assembled on top of the Grand Cherokee. They were a hassle to tie down but it worked great!