OK, I've been running it like this for a while and I wanted to share it.
These are 48 inch Yakima Bars connected to my curved roof with curved tracks from Proline Racks. The stacker is actually a set of Yakima cradles like this:
This J cradle it mounted far over on the driver side as possible and then three boats can stack on the passenger side. Additional accessories are pads on the passenger side of the bars and the all important bath mat for loading from the front, the side or the back.