The AI problems are a very common complaint. If you're having trouble with your fleet's ships running into each other, try checking out Grumpy Thumper Gaming's guides to SS, they're really helpful and worth the entire 30 mins one episode takes up lol. I was giving suggestions, not complaining about the game's combat, in fact I love the combat as it is currently, of course there is always room for improvement, but it's fine for now.
P.S: Also, it is easy to maneuver ships at the start of combat, I suggest using rally points and grouping ships together, or having frigates escort cruisers, stuff like that.