Where is the best place to get the most correct engine temp for running?

I put my temp gun on the head and check the glow plug.

POint it from the top of the head down at the glow-plug!

if you mean where to touch the sensor on the thermal gauge, the best place is at a 90 degree angle to the exhaust port just under the cooling head or if you are using a wire type sensor put it oround the head 1st flange up from bottom

I am new to the hobby and have a Pro Exotics PE-1 temp gun. Because that was what my local hobby shop had in stock.

Thats the most used temp gun So yea, just point it straight down at the glow plug.

Will it still give an accurate temp without getting that close to the glow plug?

Yep, I forget the exact numbers but, basically it will give accurate readings within a few inches or so.