I would daresay that micromanaging battles in Sins is something of a freaking art. knowing what to target when and with what def takes some trial and error, ghosting the forums, and more trial and error.... but once you get the hang of the counters, it's also important to have an easy way of ensuring your ships attack what they should when they should. The empire pane r0x for this.
The empire pane, while needing some getting used to, is absolutely essential for micro-managing. In my case I like to minimize all the planet views except where the battle is taking place. At this planet I also turn stacking off in the empire view, so each ship icon is shown (instead of group icons of each type w/ the number in that group).
Why no group stacking? Simply put, queueing attacks is essential, and with stacking off this is very easy to do in the empire pane.
Now I know there is a whole debate about focus fire vs spread fire, and what kind of impact does mitigation have on focus fire and when does it have an impact and when doesn't it have an impact blah blah blah... no just shut up and focus fire. It's easy, it's fast, and it works.
So for example let's say my enemy has a mess of LRMs and yours truly has a mess of fighters/bombers. In the Empire pane I'll alt-click one bomber icon (which will select all the bombers) then shift-alt-click one fighter icon (which then selects all the fighters and adds that to the bombers selection). So I have now very quickly selected all my fighers and bombers.
Yes this is just as easy and maybe even faster with group icons (shift click the two group icons), BUT this is where expanded view is essential (ie the aforementioned queueing attacks): with my fighters/bombers selected I first give an attack order on the first LRM icon in the empire pane, and then shift-right-click on each subsequent LRM icon, thereby queueing attack orders for the fighters/bombers.
I repeat this process for other ships (ex. heavy cruisers targeting cap ships, cap ships targeting cap ships, light frig targeting carriers, missible boats targeting turrets, etc etc etc)
As a side note a goodly sized group of fighters/bombers EAT ships and structures. They will tear through missible boats, heavy cruisers, gun turrets, hangar defense, mines, etc etc. Just as important they are FAST, so if your enemy has really spammed LRMs or even heavy cruisers, they are great for queueing attacks, since they can quickly move on to the next target. Their weakness of course is that the carriers themselves are very weak, but assuming a well balanced fleet you should be able to defend your carriers. I would go so far as to say they are an ESSENTIAL element to any fleet.
Just as necessary however is having a good balance between all the ships, but even with a good balance (and a healthy dosage of fighters), i feel what ultimately wins or loses a battle (assuming roughly equals strength) is mastery of the empire pane and smart targeting.
Using this tactic I was able to (for the first time i might add), win a battle against a superior force...