Ok I fleet my ships so they gather around my flagship, but for combat I tend to hotkey groups and issue attack orders that way.  Some people on here have said you could just order the flagship to attack and the fleet would perform its appropriate duties based on that.  So I decided to try it out against the computer and pay attention to how it worked(as per one person's suggestion I put my fleet on hold position so they don't fly off all over the place).

Beginning of game I sent a Kortul and 2 skirmishers to a nearby asteroid, order my kortul to attack a cobalt, it does what it's told.  I notice my 2 skirmishers just sit behind my cap and don't attack anything.  Later on I invade an enemy planet, order flagship to kill hangar bay, skirmishers just sit in back and do nothing.  Same deal later when I cornered a lone enemy cap.

Sooo are they just sitting there because I told them to hold position? or do they only move out to fight specific enemies?  Those of you that fight by commanding the flagship, do you have any good advice for making it work effectively?  Thanks.