You want the temp inside the egg tub to be 88-89 (or whatever temp you are aiming for). I put the thermostat probe in an egg tub with water and perlite, with or without eggs, doesn't really matter. That way my thermostat adjusts the temp for the egg tub rather than the air in the incubator.
Also, do you have a fan in your incubator? You need a fan to circulate the air, that will help keep the temps stable from top to bottom.
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