I currently just lay the copper probe in the bottom of the freezer, suspend a thermometer next to the carboy and adjust the thermostat until the thermometer reads what I want.
You're saying I should instead suspend the probe or wrap it in insulation instead of placing it in a small or large amount of water? I finally got a 7 cu ft freezer for fermentation temperature control and want to make sure I'm doing it correctly. Thanks!
You want to measure/control the temperature of the fermenting beer. Fermentation produces heat, enough to increase beer temp 5-10F under normal conditions without active cooling. You're using the freezer to remove that heat and keep the beer temperature constant.
Sensing a rise in temp of air around the carboy means the carboy is already warm enough to transfer heat to the air, which means temperature inside the carboy has already increased.
This is why I suggested the thermowell, and attaching the probe to the side of the fermentor is another option. I use both methods (I tape the probe to the side of plastic buckets).
You've got the right equipment to actively (properly) control fermentation temp; now all you have to do is stick the probe in the right place. Cheers!