For the substrate, I would try selling what you have left on CL or something similar. You really shouldn't have it in a BP enclosure at all. Sorry you bought so much...

Probes - The thermoSTAT probe always goes outside the enclosure taped to the heat source (UTH, flexwatt, etc). The thermoMETER probes, which read temps, are best placed inside the enclosure directly on the glass over the heat source. This way, you are reading the hottest temp the snake can come in contact with. The temp on the substrate should be about 1-3 degrees cooler. For example, if your temp on the glass is 95 (and it shouldn't be higher), then you want to aim for 92-93 on the substrate by adding more or less substrate and measuring with the temp gun.

Hope that was clear enough. It can be complicated to explain.