I have a resolute 2, which has the horizontal burn feature that your vigilante has. Due to the high temperature requirement for the transition from updraft to horizontal burn, I had the thermometer on top, above the baffle. The manufacturer says this gives the most accurate and useful reads for the type of stove I (we) have, due to the horizontal burn feature. (I had briefly put a thermometer on the flue, but this didn't really tell me anything useful; why do I care that the flue is 250? If the stove itself isn't holding 450-500, I need to stay in updraft.) Plus, reading only the flue will give you misguided information on your creosote level; if your flue is reading in the creosote zone, you're probably not in the creosote zone, since the stove below is hotter.
I actually removed my thermometer because I got a good feel of temperatures, and my friend pointed out that overly relying on reading a thermometer rather than the fire itself (and other things) is enabling myself. He's got a point, especially when he told me I wouldn't have a thermometer out in nature, and essentially that reading the fire, the coal, the draft, etc., is more natural and intelligent than just reading a damn number. He was right, I was definitely becoming a number-reader, rather than a fire-reader, which is what burning a wood stove is meant to make the operator into.
In regard to the damper-down position, I will tell you that if you have a good bed of coals, the air supply at or above 50% open, and holding a temperature of at least 450 for at least ten minutes or so, you'll be able to run that thing in crossburn beautifully. At least that's how it is in my resolute, but I can't see it being much different in your vigilante considering fire has the same requirements no matter what stove you have.
Their 'specially calibrated' thermometer doesn't have a 'Vermont Castings' label on it, does it? ...
