You can set the outdoor probe (the one with the wire) right on the substrate. I usually need to put something on it to weight it down so it is not moved around (which will still happen anyway).
The other thing I will do is temporarily tape the probe down right to the inside tub surface above the hotspot. This will give me a worse case scenario as to what temps the snakes will be exposed to, as mine love to move the substrate out of their way constantly. For example, I believe if i measure at the top of my substrate I may only get 88° or so, but on the bare tub im reading 92°. This would mean if I made the substrate surface temp 92°, the tub may be like 96°, which would probably be approaching uncomfortable level for the snake.