On the left side you have this nifty overview window that shows all your planets (called empire tree). It usually jumps to the planet you are fighing on, so you can use it for micromanagement. If you minimized the overview of that planet you need to maximize it again, also select "group frigates" in the upper leftern corner (othewise it's too clogged up in large battles to be used effectively) and select those ships that you want to use for attacking the enemy hoshikos. Then left-click on the hoshiko symbol that you can see in the empire tree, not on the battlefield. The fleet will now focus-fire on the Hoshiko.

Unfortunately they will only destroy one ship and search for the closest available target, no matter the ship-type again. So you will have to keep an eye on it and reassign them the target. But you won't have to search for every single Hoshiko in that cluster of ships anymore, a huge advantage already.

In your case you might want to go a bit further, select the bombers in your gravity well from the empire tree (left click on one of them while holding down ALT) and focus them on the Hoshikos. The bombers usually auto-attack various targets one by one when they could easily overwhelm even enemy caps by focus-firing. They can be even more effective than your mainfleet if microed enough.

You can also use the overview for other nifty things, you can assign planets o send their freshly produced frigates to another planet or directly into one of your fleets, you can scuttle useless vehicles or buildings without having to move to the gravity well they reside in etc...

Using shift you can assign your ships to attack different ships one after another, but unless you want to seacht that flock of enemy ships manually you'll have to undo "group frigates" again, which in turn clogs the empire tree a bit.

Just hold down shift then click on the hoshikos one after the other, your ships will kill them in the same order. If you want them to stop just give them another order or tell them to "stop" everything they are currently doing. To my knowledge there is no way of telling your ships to actively attack only one type of ships or focus their fire on one ship by themselves (although setting the fleet cohesion to "all tight" helps a bit with the latter).

Rillet have you ever been in command of anything in real life, there is some micro but general commands should be available for fleets this size? Especially when the computer bogs down with fleets this size making micro impossible and giving the advantage to the enemy.

Anyways, I just kicked the AI's ass and found a small bug.

String no found after playing on past a military victory as the advent and a repeating voice saying something like "yay the advent won" forever.

Where do I get my space cookie? Also how do I get a space ponie   

So frigates are the ticket then... unless as the poster above said I divvy up my fleet into 10 smaller fleets and micro like crazy.