For a HERMS I believe that the best spot for the temp probe controlling your heat in the plumbing, output of the heat exchanger.
That being said, its nice to be able to see what the grain bed is doing as well. Ideally its the same as the output of the hex, but in reality thats not always the case. I mash in a rectangular cooler, so I wanted to be able to hit the middle of the bed from the top so I didn't have to make another leakproof hole. I took a BCS-460 probe and stuck it in a 3/8" copper pipe, and connected it with a brass union. That way I can stick it anywhere in the grainbed, and even check multiple spots if I want.
And I can use it for fermentation temperature monitoring/control in a carboy too. The temp stick works better than a thermowell, imho. Plus its cheap.