I always just put them on top of the rock in the past. Never had a problem (that I'm aware of). The nonpen sitting on a rubber pad puts fewer PSI on the roof than a person walking....so theoretically if you can walk on it you can put a non-pen on it.
One landlord required me to sweep away the rock first. Same landlord required a sacrificial piece of EPDM roofing in addition to the rubber pad that we always used....so IMO he was a little paranoid.
Thoughts on pros/cons. When putting a Non-Pen on a roof with river rock, (if that's what it's called, 1/2"-1" diameter stones, no tar) do you clear the rock and put the non-pen mats directly on the roof, or put the mats and non-pen on top of the rock?
