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 that's 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 sid
As explained previously I load both of mine over the bull bar with suitable protection on the duco. But scratches aren't a worry for me. If I had a new vehicle I would use a 'rock & roll' side loader or a home made device like StI's suggestion. (just carry a bit of dense foam or such like for the lower end protection when swiveling the raised end into position).If you choose to carry them right way up, the scupper holes should drain away most of any water but not so with SinKs which I believe go in a cradle the right way up with suitable covers over the '****pit'.