I spoke to Bob at Pro-Products about this type of setup. I was told to dangle the probe just off the floor 2-3"s on the cool side and look for a target cool side temp. I'm at 81 degrees. That allows my hot side to stick at 91-93 degrees. I do not have the probe touching any surface.
So basically I'm setting my target temp for cool side temp. After a little tweaking, the cool side is a consistent temp 81 and the hot side only ranges 91-93 which is perfect. The cage is big enough for the snake to choose his location. I find he uses both sides equally.