the gunwales of the PA are a decent place to put load also, but be judicious of sliding it upside down. You can allow it to rest on bars without much if any padding. I had three on my trailer for two years and carried the third upside down on the overhead rack. It worked fine and kept me from having a full length spread like on the hull down units. One bar was just inside the footwell behind the front hatch and the rear bar was mid tank well area.
Just pick your placement carefully and get help putting it up if possible. I only trailer mine ( I'm down to one yak for a while) now and while it isn't as convenient for getting on the road, it is really nice to load it up the night before a trip and only have to load the heavier things when I get to the water.
Good luck, Phill