You want the hottest place your snake can reach to be 90. Since your snake can and may burrow under the substrate for additional warmth, you want the glass under the substrate and over the heat pad to be 90. It's OK if it's cooler on top of the substrate. You don't want it 90 on top of the substrate and 100 under the substrate!

To test this just move some of the substrate aside and measure the temp of the glass beneath it. Good job using an infrared thermometer and a thermostat!!