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i will tell you what i have been told to do and am currently doing...
put the cool probe in the spot where the reptile is going to spend most of its time, and the same goes for the warmer end, it has been recomended to me that you put the probe in the hide... mine is about 2mm behind it.
Another way you can do it is you can simply monitor the average Temps, place a single theremometer probe in the middle of the enclosure, about 3/4 of the way up the side and monitor the averages that you particular reptile needs...