I got a new digital control pack that came with a through the wall thermowell with a solid front on it. Since I have to redo some of the plumbing anyways I was wondering if the trhough the wall thermowell is better or if a 90 elbow with the thermowell in it is better?

I prefer through the wall, assuming it's not a drywell, but where the thermistor is in direct contact with the water.

Either one will work, but through the wall is a bit more accurate and precise.

My pack came with a drywell. Can you recomend a suitable one where it would be in contact? The sensor I have is an eletronic one with a small cylinder about 2 or 3 inches long.

Something like this?:

http://spapartsnet.com/Thermowells-Heat ... 2_1_1.html