Just purchased one myself!

The rack just clamps onto the roof on either gutter, if you lift the rubber seal on the inward side of where the > < marks are, the 'J' just slides in there, then when you tighten up on either side it actually clamps onto the roof. You don't have to do anything with the rubber seal as it should just about lay down play again over the top.
Here's a pic of mine although you can't really see the fitment.

Edit - this is the Votex rack, just in case your's is Thule or something!?