The draft is usually checked at the chimney breech. It really isn't critical where, almost anywhere in the stack will work. I use a probe style thermometer at the elbow to the breech. When I want to read the draft I just slide it out and stick the tube in. A piece of steel brake line works well. You'll need to calibrate the manometer each time you use it as they are very sensitive to changes in atmospheric pressure.
If you are measuring the stacks temp on the surface of the pipe, it is a lot lower reading than what is at the center, it could be 100* higher there. That is why the anal retentive types prefer the probe (
), it gives a more accurate reading.
I'm not familiar with the LL Hy Fire, you should double check with them about the barometric. I would always install one, but on some stoves with exhaust blowers, it can be very dangerous.