At first, don't overstress the micro management of battles. The game philosophy is to let the AI take care of most of it.

Later on, yes.

The AI is very limited compared to what a human can do.  I barely trust the AI to do anything right in this game, which is not to say that the AI is bad as far as computer game AI goes.  Rather, it's just hard for AI to weigh the hundreds of variables and to see the big picture like a human can.  I wish that there were an option to set enemy ship type priorities for each of your ship types so that if the AI is in control it attcks the stuff you want it to attack.  (I see this same problem often in the early game when I'm colonizing and, if left without orders, your mothership's strikecraft will start attacking militia flak frigates (which are anti-strikecraft).)

Anyway, once you've learned about the in's and out's of the three races and feel comfortable with the mechanics of the game, you'll probably tire of playing against the AI (which is awful compared to human opposition) and want to come play the game in online multiplayer.  You just click the Ironclad Online button, create an account, and come join the fun.  Note that you can also play humans v. AI games called Comp Stomps which can be a good way to learn from other people and to enjoy having human teamates and camraderie while you're learning the game.

The biggest issue for AI targeting are fighters, as they tend to go after other bombers.  In reality, you want your fighters to target enemy fighters, bombers, and long range frigates relatively evenly.  This can be a pain to manage.