AstroBee. Very common thinking. First of all in a chamber as small as a typical queen cell incubator the temperature at the cells will be nearly identical as that at the heat source. But lets assume that you are correct and that there will be a difference at the cells hang their is at the heat source. The more accurate way to control this is to have the heat sensor at the heat source since that is what it is controlling and a thermometer at the cells. If you set the controller to 95 degrees but the thermometer reds 90 degrees at the cells. simply increase the temp the controller is set at.
Keep in mind no thermometer sensor or controller is goign to achieve the proper temperature. None are reliable. I never have just one thermometer and I only use thermometers that agree in their reading when set side by side. So do not think you can set a temperature controller to 95 degrees and then think you will in fact get 95 degrees. You have to measure it for accuracy.
SO why is it better to have the sensor at the heat source/ Because if you move the sensor away from it the heat has to build up until it reaches the sensor. this will cause the air near the heat source to actually be over heated. Remember it is energy in energy out. and you end up over energizing parts of the incubator. This over energized air will spread across the incubator and cause a temperature spike. as the air cools it will also tend to fall below the correct temperature more also. this is because there is more of a recovery necessary when the sensor is further from the heat source. the entire chamber has started to cool off and the heat source cannot catch up quite quickly enough. this may or may not be a problem depending on you specific design. There is also a period when you first start up an incubator that it will over heat then under cool . but each time it cycles it will be over or under by fewer degrees. it is something like a pendulum swinging back and forth. but let it set for a while and it will stabilize. If you still have a swing in temperature ti will become very close to equal above and below the set temperature. Once you see that you have seen just how accurately your design can hold a set temperature. Shorter more frequent bursts from the heat source produce a more stable temperature than a longer but less frequent one.
You can place your temperature sensor any place you prefer. but I do recommend you try different locations and take careful measurements so that you are aware of what happens with the various placements. In my case the swing in temperature of having the heat source just 6 inches from the thermostat was enough to kill Serama embryos. Queen cells are not nearly as delicate. In my 4 cubic foot incubator I place the thermostat 1 inch from the heat source for very tight temp control. in my 22 cubic foot incubator it is 3 feet away. Exact temp in the big one is of little concern. In my queen cell incubator I actually place it just about anywhere and then set the temp according to thermometers placed right on top of the cell cages.
If temp swing is not a problem the n none of these measures are necessary. but when swing is a problem it can be frustrating to get figured out. So I added this info for those that may need it.