Yes, the probes go inside the enclosure on top of the substrate. You will want to be testing temps on the floor because that is where the snake will reside. When using a UTH, some people put the probe under the hide where it can be much warmer than the rest of the cage, and this is where the snake will most likely be spending most of its time. What kind of thermostat are you getting, and what kind of heat source are you using?