you can still have your probe on the inside of the enclosure(which is what I do). That way you get a reading of what temperature your snake is getting. At the same time just set your controller a degree or two higher because it has to warm up past the glass and substrate. Just make sure you use the thermometer to read inside and you’re fine. Outing the probe between the heat mat and glass, or on the inside of the enclosure really doesn’t matter, because at the end of the day you can change the set temperature on the controller to get the desired temperature within the enclosure.