yea i remeber sort of. for the truck that came with the racks it looks like they had the screw in area molded into the roof. what i would think is since your going to put holes in the roof anyway, why not look for those (try to visualize it lol) they are nuts but have a small section that comes up and looks like a washer on the end. (did a search but coldnt find what i wanted. look at the pic below drawing in paint is tough enough doint it with 1 arm that isnt your dominant really sucks)
just drill the roof, put some sealant on the washer part then thread the roof rack bolt into the nut and it should make a seal that will be strong but also waterproof.