Some folks are putting racks directly on the freedom top, but if you read the manual, it will tell you it is not intended to carry a load of any kind.
I'm looking at the Congo Cage
from KargoMaster. It attaches to the side of the windshield and to the rear bumper or frame (depending on bumper). They sell brackets that adapt Yakima or Thule crossbars.
I think my tandem kayak will look pretty nice on top of my 4-door JK!