1st...If you're using only one egg box, then definitely put the probe in the egg box. If you have more than one egg box going, then its probably best to put the probe in the center of the incubator. If you're using a "walk-in" incubator, and using the very large "egg boxes" (Barkers use trash cans, others use styro shipping inserts), then the probe in the middle of the room is fine.

Keep in mind that eggs start to generate quite a bit of heat in the last week and a half or so...If the probe is outside of the egg box and the thermostat is set on say 89, it could be quite a bit higher inside the egg box (I've heard as many as 6-8 degrees or more). I'm a firm believer that this is the number one reason for the "full term dead in egg" syndrome that some folks have experienced from time to time.

On another note...you mentioned the probe making the egg box "not air tight". That's actually a bonus. Egg boxes should not be air tight. They should have a snug fitting lid, but should not be 100% sealed off from the outside air...

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