They never did respond to my email from 1/17 so I called them today. They say that it can be set up either way with the latching...they recommend closing the cover on top of the tailgate as you get a better seal, but it can be done the other way as well.
As for the leaks, her advice was to make sure that the side rails and weatherstripping are absolutely even with the top of the bed rail (which mine are and still leak some), and also make sure track rails do not tilt to the inside. Or else you get channels where the water collects and leaks in...so I may need to tighten mine down more or get some additional clamps.
I was hoping for better information...I did express my disapproval at the lack of instructions with regard to installing the cover itself. She had no response to that.
Red Hot Trail Boss