I have done both, set up at the lake and cartop, and it is no big deal either way. I have a Creek Company ODC 816 and I have always kept the pontoons strapped to the frame, even when I trunked my boat and set it up at the lake. Putting the boat together and inflating it takes only 5-10 minutes depending on how many Red Bulls I had in the morning.

I currently car top my boat because I have a place to store the boat fully assembled and a roof rack on my Subaru. It takes about 5-10 minutes to strap it to the roof. I use four small cam-straps, one on each corner of the boat and it rides great at highways speeds (65-80 MPH)

If you have any specific questions post the here and I will do my best to answer them also, you may want to re-post this question in the float tube forum

Lotta ins, lotta outs, lotta what have-yous