I would be VERY concerned about having the thermostat probe and heat mat inside the enclosure at all. That being said, if you have eliminated the risk of the heat mat causing an electrical fire (spilled water + electricity = bad), I would place the thermostat probe between the mat and the bottom of the enclosure to minimize the risk that the BP moves the probe and the mat becomes unregulated. Neither the thermostat or thermometer probe EVER go on top of the substrate, because then you are not regulating the temp at it's hottest point (direct contact under the substrate).