What I did for car racks on the gutterless cars is to take a 2x6 and shaped the edge to closely fit the top surface of the edge of the roof. Then I covered that shaped surface with a layer of closed cell backpacker's pad foam. The cross bars were 1" thick by 2" wide oak hardwood flooring strips, and I usually used 4 to 6 of them. Because the cross bars were a hardwood, I pre drilled and counter sunk the holes for the screws used to attach the cross bars to the tops of the side rails. Then I used 2 straps on each side with flat plate hooks to hold it down to the door opening. The hooks were around 1.5" wide, and were made out of stamped and bent sheet metal. The strap went through the hole in the hook, and a pair of holes drilled in the side rail. Keeping the holes in the side rails low helps the hook hold better. I've carried a 16' long wide bodied Smokercraft on many different small cars with that style of car carrier.
Hooks looked something like these, but simpler:
http://www.rightlinegear.com/roof-cargo ... ories.html