I keep my probe under the loose substrate... I do either paper towel or reptile carpet directly on the glass because I felt weird about her touching straight to the glass if she did decide to burrow.... and then on the hot side I have a very thin layer of Eco Earth substrate over that (little thicker layer on the cooler side)

My thermometer probe is on top of the reptile carpet, but UNDER the eco earth since like previous posts said, the snake could burrow under that part of it if she wanted

I keep my thermostat for the UTH set at 94* because the layer of reptile carpet blocks some of the heat.... that makes the surface on top of the carpet pretty steady at 90.