Transporting a sit-on top kayak is very easy.

You basically place it onto your roof racks upside down and secure with a couple of tie-downs. 

Normal roof rack bars are all thats required for one kayak but if you are looking at taking 2 kayaks regularly then it might pay to get wide roof rack bars (1500mm) so that they can lie side by side or you can use Fold-A-Poles whereby the kayaks lie on their sides.