The fist rule of giving commands in Starsector is: don't.
At least not when you're not trying to archive something very specific. In normal combat, the AI is competent to make its own decisions. Sure, you can use the "eliminate" command just to choose your next target, but your fleet will choose a target anyway. Your ships will take more risks when you put aggressive orders on them ("eliminate" or "full assault"), so this is safe only as long as you have superior strength anyway. Then it can end battles a little quicker.
In a pitched battle, use eliminate only to take out specific threats, for example a carrier or missile ship that you can't properly defend against.
If there's some really scary ship facing you that you can't take out with "eliminate", it might be best to issue an "avoid" oder on it, so you take out all escorts first so your entire fleet can focus on it.
On your side, it might be worth it to issue some escort orders. For example, I like a purpose build PD frigate to escort my flag ship. That way, when I overload, it will keep me (more or less) safe from the inevitable missile barrage the enemy will send my way.
Same is true for other valuable ships, especially when they have little PD themselves.
You can't command fighters directly anymore, just the carriers.