Why didnt you just ask me?
I have my temp measured IN the HLT cooler (HEX).
My pump ALWAYS runs during the mash.
The PID would only turn on and off the element in the HLT (HEX).
There is a temp differential between the HLT (HEX) and the MLT, and if you are truely buidling a "clone" of my system, that differential will be 3-4 degrees F.
I measure the temp in the HLT (HEX) for this reason.... I do not want to heat the MLT any higher than it needs to be raised, otherwise I risk an overshoot in my MLT. If I measure the HEX output, it is better than measuring the HLT output, but it disregards the ACTUAL temp in the HEX. Depending on the rate of flow of your recirc. Example:
You command 155F on the PID.
Your HEX output is 152F.
PID turns ON the heat...
By the time your wort is exiting at 155F your HEX temp at this time could be 160F... so if you do NOT turn off your pump, you will eventually heat your MLT up to nearly 160.
Bottom line is, you do not want to have your HEX temp allowed to exceed your target temp, unless there is a differential between the HEX and the MLT due to wort trasfer throuh pumps and hoses, like I said, in mine that is 3F. If you allow the HEX temp to get above that, then you have to sit there and turn the pump on and off, or a PID has to, so why not have the PID control the HEX temp instead, since you want to control that temp too?
Mine works like this. I strike at the appropriate temp, say resting at 155F. Top up my HLT(HEX) with the appropriate ammount of water to settle it at my recirc temp, in this scenario 158F. (this is a computer calculation that is too complex for me to do alone) I open the valves and turn on the pump with my controller set at 158F, that is the temp as measured in the HEX. I leave the pump on and walk away for an hour or so. I come back and the mash is complete with a temp variation of about .5F as measured by my through the wall MLT therm.
If you do it this way, you will never, NEVER EVER overshoot your temp, you will not have to turn off and on your pump in your MLT, you will have constant recirculation of wort flowing through your grain bed to assure no temp stratification. Also, if you STOP recirculating and have your PID probe in the HEX outlet... that wort in the outlet will cool significantly in a short time, commanding your PID to heat again... the next time you start your pump the HEX itself could be 190F. The PID really needs to know the HEX temp IMHO.