The thermostat measures the tape thats being heated and pulses the power as needed to maintain the temp you have set. However, if the desired temp is 90 degrees on the inner tub surface, you may have to run the thermostat at 92, 94, etc., because some of the heat is lost in the transfer through the tub material. Raise the temp on the thermostat until the temp of the tub is where you want it to be with the gun reading. The temp gun is the more accurate of the two devices between it and the thermometer. The gun is good within several tenths of a degree.
Now once you have the temperature where you want using the gun, your thermometer may not read the same, but it shouldn't fluctuate all over the place. If you heat is stable then the thermometer reading should be stable. However, if your thermometer doesn't read the same as the temp gun but is within a degree or so, then just note what the reading is and use it to see that the temperature remains constant. In other words if once you have a reading with your gun at 90, if the thermometer says 92, just make sure it stays at 92. If it reads 88, the see that it stays at 88.
Trust the gun and monitor with the thermometer.
I hope that helps
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