I will focus on the battle only so much as to send capital ships, bombers and anti-structure cruisers towards any starbases, and the rest of the fleet towards everything else (I found this minimizes losses of frigates/cruisers). Past that I reply on the ships' basic programming to clear the gravity well for me. A well balanced fleet, with some creative key assinments, can take on anything.
I perfer large, 50 plus planet maps. There you can get away with just sending your fleet somewhere and letting it do its thing. On smaller maps you must keep track of your ships, as resources are more scarce and enimies more close. The rare occasions I play a small map, I think of each gravity well as a single map (where one has to pay more attention to individual units, orders and locations).
For large fleets I have multiple hotkeys:
"1" - Main Assault/Core Fleet: a well balanced fleet capable of complete autonomy. Caps, frigates, cruisers and anti-structure.
"2" - Secondary Fleet/Support Fleet (Reserves/Nat'l Guard): another well balanced fleet, about 1/3 to 1/2 the size of '1'. Better suited to defensive purposes. Caps, frigates, cruisers. Lacks anti-structure support.
"3" - 1 & 2 put together
"4" - just the capital ships from 1
"5" - just the frigates/cruisers from 1
"6" - just the anti-structure cruisers from 1
7,8,9 & 0 -tasked to construction cruisers, coloney frigates, and scouts as needed.