If you're referring to the rear windows, they go under. Everything goes under, except the part of the windshield that goes in front of the cabin braces and the part that attaches to the leading edge formers. btw, if you're using CA for the windows, use sparingly. CA fogs that clear plastic like crazy.
Bit of a tip here, I tried putting monokote on the window frames without much success. Just too hard to get a good seal with my iron in those cramped spaces. So, I stripped it off and found matching paint for those. Saved me a lot of dog kicking. Another plus for electrics: No fuelproofing necessary.
