Peel the Reptitherm slowly from one corner until you can get the probe in the middle and stick it again. You can use foil tape to keep it stuck again.
One of your thermometer probes should be under the substrate, over the hot side, touching the glass. This one should read 90-92F. Your other thermometer could be a couple of inches above your substrate measuring ambient temps. This should be 79-82F
If you can get a second thermostat for your lamp that would be great!
.5 inch of substrate is just fine.