You can put styrofoam between the heat mat and whatever you have your tank on. That will help the heat transfer to the tank a little better, and also protect the surface below. I would cut a few holes in the styrofoam to let it vent, but probably not necessary.
A thermostat should keep the heat mat well below any temps that can hurt the surface your tank is on, but in case of thermostat failure, etc. it's better to be safe than sorry.
Finally, the thermostat probe goes between the heat mat and the tank bottom.
If this isn't clear, let me know, and I'll try to explain better.
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