The Fighter Tactics skill under the Leadership attribute provides you a straight benefit in Command Points solely for use in commanding fighters. In combination with CIC Officers (who normally possess this skill), your fighter command points would simply appear beneath your main command points display as a smaller "surtitle". Whenever you command a fighter wing instead of a larger ship, you draw from the pool of fighter Command Points first, leaving your command points for larger strategic initiatives.
I would recommend Fighter Tactics having a measurable benefit in command points, likely +3 Command Points per level for fighters only. At maximum level, if you wanted to be that crazy, you could have a whopping 30 Command Points to allow you to micromanage your fighters to your heart's content. Or, if you didn't care at all about it or don't want to micromanage your fighters, you could simply ignore the skill and let your fighters do their own thing as always.
