Go here, and look at the section about "Reference Files & Conversion Tools" to figure out how to do all that....the very top of that thread also I believe shows to to make a mod in general...

The entity files you will most be interested are the ones who's names begin with CAPITALSHIP...open those, and look for the line "CommandPoints"...underneath that, you can set the starting value as well as the per level increase...for example, if the base value was 3.5 and the per level value was .25, then that particular capital ship would start with 3 SC squadrons and get a 4th when it reached level 3 (2 level increases)...values truncate/round down, so 3.9 squadrons is still only 3....