Always measure surface temps. Your surface temp will be the highest temp in the enclosure, and your snake will most definitely find it eventually. So you want to avoid that spot getting too hot and risking burns to your animal. So, always measure under the substrate regardless of what substrate you use. Think of it this way: If I use coco husk 3 inches deep and my snake burrows, it touches the glass. So wouldn't I want to know that temp? The same applies to a 1/8 inch layer of paper towel.