I don't think it is great to leave the sensor in the air. I have also been searching for the best answer to this problem.
What I do.
- I only do SMD boards, no thru-hole.
- I place the boards on a copper sheet that I tarnished so that it is mostly black in color
- I stuck the thermocouple onto the copper sheet and cover it with aluminum tape. I've also tried soldering the thermocouple to a hole in the copper with extra-high temp solder but couldn't get this to work well.
- I place my boards close to the thermocouple and observe the feedback temperature during the cycle at the same time as watching the pcb to catch the temp at which the solder flows.
What I have noticed is that on really small boards the solder melts almost perfectly at the same temp as solder melt temp. On larger boards I have seen as much as 15C different but typically it is 5C or 10C. In other words, the feedback will show a copper sheet temperature of 195C when the board flows. whatever the feedback temperature is, I make a quick adjustment in my head as to when I will open the door.
My solder joints always look really good and i have not burned any components.
If you want to get really obsessive you can solder a thermocouple directly to the PCB with silver solder. I've done this and of course you get nearly perfect temperature feedback. However, this is really not a practical approach to making boards and I don't think it is necessary.
It can also work pretty well to connect a thermocouple to a spare blank PCB and place this next to the PCB you are building. I did this method for a while but eventually decided I didn't like the look of that one PCB getting cooked over and over again.
here is my write-up on how I made the copper black.
http://themzlab.tumblr.com/tarnishing