You should have any heater probe positioned in-line with the centre of the heat source and halfway between the heater and the ground. You want to ensure the heat source is accurately controlled and not the ambient temps or the cool side temps. Calibrate the basking temp with an infra red temp gun.
The ambient and cool side temps will be on point as long as the wattage of your heat source is what is recommended for the size of your enclosure. This is because you want to have the basking area set to a certain temperature that dictates the rest of the cage temps.
For example I have my baby Burm in a 4 x 2 enclosure. A 150 watt heat source is the sweet spot for the size of my enclosure. So as long as my heat source is controlled by a pulse proportional stat all other enclosure temps fall in-line irrespective of external room temps within reason