1. The probe works best if it is in the beans. How you do that is up to you. In a popper with a can on it I would drill a hole in the can.
2. Pretty accurate and far better than your milk thermometer.
3. Stick a foam cup over the group-head and stick the probe into the cup.
The probe is about 7cm long, you can see it at the bottom of the picture in BeanBay.
Only the last few milimeters (maybe 4mm) do the actual work.