You don't have to lift a finger or do a thing in terms of the space battles if you don't want to. The AI will fight the battles for you. And even if you do micromanage it's still more of both sides face off and fire at each other.

But if you want you can get "down and dirty" and direct every ship to do your orders. Typically all I do is if the battle is in question and it's an important one I'll do things like direct ship fire to a certain capital ship I want to take out or perhaps all I really want to do is just knock out the shipyards or research stations in the system then I'll direct my fleet to do just those things and just jump out.

I have had multiple battles going on at once and only "micromanaged" one of them. You can keep on eye on your ships status on the empire tree and if you see a lot of them turning red then I'll zoom over to that battle and do something about it or not even do that as I can click the fleet icon in the empire tree and issue the "retreat" order and that fleet will jump away to the nearest friendly system. Meanwhile I'm watching this other bigger battle and issuing orders if I want.

So it is definately not a click fest at all. In fact that is a complaint of the hard core RTS "twitch" gamers is that they don't like Sins because it's too slow for them.