>>In the egg box like I here a lot say or the middle of the incubator.
I put my probe inside the egg box. Towards the end of incubation, (I've heard) eggs generate more heat. (How much more, I don't know and never really checked. This might be interesting to know.) I don't worry too much about eggs at different stages. Temps are not absolute or set in stone. I set my temp to 91 (interestingly enough, they do not hatch any earlier than if I used 89). Once one egg box begins to pip, I move the probe to the next egg box. I have had no issues with overheating and my incubators are fairly consistent throughout.
I do not keep my egg boxes air tight. I also open each box once every 10-14 days and air out the egg box. I never put the probe in the air in the middle of the incubator. Air heats and cools at a much different rate than things like eggs and substrate.
>>i here the pro's don't STICK IT in the tubs just in the incubator center and get great results.
Kind of hard to put the probe in with the eggs when you have 200 clutches. 
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Jay A. Martin
Jay Martin Reptiles