The only dumb question is the one not asked.
As I understand, you dangle the probe about an inch or so above the substrate on the warm side under the CHE. That way you measure ambient temp and the snake can't move the probe significantly. You use the temp gun to measure the temp of the substrate and under the hides.
It'll take some fiddling to get it all correct, but it's very doable.
What kind of thermostat you looking to upgrade to?