I know they get a lot of flack but I have found a couple of things you can do to maximize their utility.
1) Keep targeting: Once the primary target is destroyed, they will attempt to dock with you. The key here is to be in weapons range or an enemy <10k so they re-acquire instead of dock.
2) Keep Your Distance: Don't Let Them Dock - I have used evasive maneuvers or an engine battery to run away before they dock so as to give me time to acquire another target. I have easily spread out their lives long enough to be able to deploy a second batch.
That's pretty much it. If this is already old news, then accept my apology, but I have found these fighters actually a little hand and fun with proper management.