Ok. I'm not sure I'm reading your question right, but we'll see...
The probe goes outside the enclosure sandwiched between the UTH and the glass/tub.
The UTH should be stuck to the bottom of the enclosure (you may need to use aluminum tape)
The enclosure should be slightly elevated from the surface it's on to allow for airflow.
You should be using your temp gun to measure the actual surface temp, not the substrate.
Your tstat could be anywhere from 2-10° different from your actual surface temp. It's just a matter of trial and error with no one answer due to tons of variables.
For BPs you should be aiming for 88-89 for a hot spot.
I hope this helps. If not please feel free to follow up and I'll try to clarify. I kept my reply vague, so please forgive if I was too vague