Here's what I tend to do...
1. Skirmishers: I like to use them, but mostly as a support ship rather than a combat fighter (although their attack value does help).
2. Subverters: I'm not much of a micromanager, so I tend to leave the distortion field autocast on. However, I usually turn it off if there are a lot of civilian buildings (my subverters especially like to shut down labs for some strange reason), or if the enemy fleet is mostly capital ships (distortion field does not affect capital ships).
3. Overseers: I tend to have about 14% of my fleet as overseers (I normally have 70-80 ships to a fleet, so I have about 10 overseers). It may seem like a lot, but they are really useful (for me) when trying to take out large fleets. They're also useful during starbase matches. If they like to wander, I set the fleet formation to a slightly tighter stance. In the end, it pretty much boils down to personal preference and style of play.
4. HC: I don't spam them, but I do make a decent amount. They pack quite a punch, and are excellent at keeping the enemy right where you want them. They're also great if you have a starbase in the same well (gives the base some time to catch up).
5. Starbases: I like to get one up ASAP (without breaking my economy). If you find a good chokepoint, don't hesitate to get even a mediocre starbase up. Two or three well chosen upgrades on a starbase in earlygame are more than enough to make someone stop and think.
Lots of luck.
