if you go with an MIP, you should loop the thermistor around the lowest possible cut in your heatsink/head. That is, you want the sensor to be as close to the engine block as possible. This works better with some heads than others (for example, it works fine on an O'Donnell head, but its sometimes a problem on the OS heads).

With a temp gun (I use a raytek) you bring the car to a stop, then point the gun down the top of the head so it is reading from the top of the glow plug, then pull the trigger to get the temp. Its important with temp guns to make sure that you have the lens of the gun as close as possible to the top of the cylinder head, and its equally important to point the gun straight down on top of the glow plug.

On this board you will typically find people talking in terms of Farenheit, although the raytek (and some others too) has the ability to switch between F and C.

Most people suggest running in the 260 F range. Thats just a general engine health guideline. Generally I tune for power, then make sure that the temps are in an acceptable range. Temp alone doesn't mean your engine is tuned, but an excessively high temp will almost gurantee an early death for your engine.