Well, I tried to find a thread posted recently that had some discussion on this. I'll just toss you what I did.
The stock therm does not like water, and has a fairly short stem. Water vapor will condense into the case and cause problems if exposed too long the wrong way. It will get behind the glass lens as well.
I take a fryer therm or digital probe and check it in boiling water. Don't submerge your digi probe too close to the top of the probe, water can enter the top where the cable goes into the tube, and possibly cause a short-circuit.
Depending on your elevation (barometric pressure) and weather activity, water boils at 212* at sea level, then slightly less at higher elevation. With a digi they are pretty accurate. Check your probe temp reading in boiling water.
You can pull the stock thermo back out and rotate it 90 degrees and hold the stem into the cabinet, while you put a thermo probe into the cabinet through the pin holes for the stock thermo. Fire up the burner and bring smoker up to a reasonable smoking temp (220 or so). Keep both thermos in the cabinet until readings are stable.
If stock therm reads low or high, you can adjust it with the hex "nut" on the stem next to the back plate. I think it's a 7/16" SAE, or use an adjustable end wrench. Adjust up or down to match your probe. Re-check the reading again, and repeat these steps if needed. You may need to wait until the stock therm cools to adjust. Then, re-check.
Someone mentioned, maybe in another thread, that the stock therms may not be accurate throughout the range of temps. This is correct. Most stock therms are kinda "tempermental". If you calibrate it at close to the range you will be smoking at, it should give the best accuracy.
Hope this helps, good luck, and enjoy that new rig!