The probe should be inside the tub, under the bedding. Depending on your thermostat u may be able to calibrate it so that when your Tstat is set to 88, the inside of the tub reads 88. Just be sure to pay attention and check it a couple times a week or so for accuracy-the Tstat is reading the temp of it's probe, so it seems that it's functioning properly.
I'm glad you use one and even happier that you're ensuring you're using it correctly. It's always nice to know we've got good snake parents out there!