I would follow the directions that came with the rack on installing the flexwatt, This thread should help as well:
http://ball-pythons.net/forums/showt...ck-build-video
The probe needs to be on the middle shelf
I could stand on top of my AP rack, I'm fairly certain that your gecko cages will be fine.
AP racks have a pretty tight fit with their tubs... I wouldn't be too worried about escapes