I use a roller with a couple of guides on each side to pull the kayaks up, then when up there I use a standard gutter rail mount with long bars. To keep the bars from sagging I put some PVC pipe in the center. You can see what the roof looks like below:

When loading I just stand the kayaks up on end leaning on the roller, it won't topple because it rests on the guides. I climb up the ladder and pull it up nose first, then the move the first kayak over to the passenger side and the second stays on the driver's.

Then I just strap it down upside down and they stay there just fine. Not a significant increase in height over the A/C unit, maybe two or three inches (and the antenna is taller than that). I can do it all myself as I rarely have someone around to help, but it is easier with a second person.
Joe