We bought our Thule set-up from Rackattack.com. Wicked pissa cheap (they're based near Boston)...four boards or two boards and four sets of skis...for just $99. Included everything, including the clamps. Of course, we already had the crossbars on the SUV, so you'll pay some more for those, but still their prices can't be beat.
As for folding down the seats...do it if you can. We stopped putting the boards on the roof because the loaded racks caused so much drag that we'd literally lose like 4 mpg on the average trip to Vermont. When you're traveling a 3-400 miles, that adds up. Even if we bring a passenger (or two) in the back seat, the 60/40 split seats fold down to accommodate all our gear.