I have trouble with this, too. My tanks are raised about 1/4" above the heat pad, with the thermostat probe on the heat mat, but the mats are taped down to the stand, so there is a good 1/4" between the tank and the heat pad, and add in the 1-1.5" of substrate...it's tricky. I use a mixture of substrates that compact and can't be manipulated, and nestle my thermometer probe into the substrate so it's about .5" from the glass... I usually set the thermostat to about 97 or so, but it's been colder here lately so I have it up to 105, and it's now sitting at about 91 in the tank ( so it's slightly cooler on top of the substrate, where the snakes are).
Dunno if that will help you, but it definitely takes some tinkering...
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