Fish It :
Yep I have always stored the boats on the car right side up (just seems easier to me). Especially with the TI because it has the metal AKA bars it would scratch the car. We live near the water, so most weekends I just get the boat out of the garage, throw one of those big (about 3 1/2 in dia x 4 ft long) pool noodles on the roof just in front of the rear cross bar. I then put the Tbar into the hitch, lift the front of the boat onto the Tbar, then slide it forward. The boat rolls on the pool noodle nicely. I then strap the boat down to the cars roof racks, and I'm off sailing, it takes at most ten minutes to load up and strap down. Now if the boat is going to be up there a while, I will add a couple small noodles along the sides lengthways just for stability, and more support area if sitting on the top of the car (sometimes for several weeks at a time). We drive down to Key west every month, and I usually add the side noodles, and a couple extra straps for the 350 mile drive.
We started kayaking alot in 2007 and have over 120,000 traveling miles on the cars since then (we've worn out 2 vehicles, and are on our third tow vehicle now (the Denali in the pic.). Like I said when we travel we always take our boats along. I haven't lost any boats yet (knock on wood).
With our old Malone rack system the boats sat much higher, with this setup the hull is much closer to the car and I think alot more stable in the wind.
I believe a couple companies sell padded covers that fit over the standard roof rack cross bars, you could probably do away with the pool noodles with those on lighter boats. On a boat like the Revo or outback, you could probably flip lighter boats upside down once it's on the roof, if you prefer.
I'm not recommending any one type over another, I'm just discribing what we have, and how much we like the T-bar hitch mount, which works nice on our vehicle, and our boats.
Hope this helps
Here is a pic of my TI on the car just leaving to go out sailing.