Are there any campaigns in this game?
Nope.
Is there a way to label fleets?
Nope.
And how do i designate a ship as the flagship in a fleet?
Make sure that the ship that you want as the leader is highlited in the empire tree to the right. Use either tab or shift+tab to scroll through your selected ships. Now when you press the fleet button it will use the highlited ship as it's leader.
