From: The Big Nowhere
When I first started playing I was overwhelmed with battles too, it felt like too much was going on.
I handle the universe by creating fleets that are named after their home or easier, grid sector i.e. 'Defence Fleet E3'.
I then set the fleet posture to defend that sector and automate.
I ignore civilian and explorer ships getting hit in battle. The natural expendable casualties of war.
I then create 2 to 3 'attack' fleets that are not set to auto and that I control myself doing raids and strikes in cycle, refuelling whilst another fleet runs in. This leaves you to concentrate mainly on offensive action and let the defensive fleets take care of your colonies and sectors.
Don't forget the left hand menu listing enemy targets, that helps and also shows what fleet is attacking what.
Finally I change the alarm sound to something a lot quieter and more subtle!
I hope that helps.
I fix the explorer thing by redesigning them with guns, a minimum speed of 50 and shields. Set to stand-off and flee at shields 50%. They can take care of single escorts, space slugs, etc on their own. Really makes things interesting.
On freighters, unless something has changed in the last patch, you can put as many point defense and Ion Cannons on them as you like (meaning they can get away since the Ions temporarily disable targets). On the other hand, you make a lot of money building replacement ships for the private sector, so weigh exactly what you want to do carefully.
Distant Worlds Fan
'When in doubt...attack!'