not sure exactly what to say as i'm not sure i understand exactly what the question is. i'll share my own technique for fighter micro, hopefully you'll find it useful.
first thing i do is make a subgroup for my fighter squadrons. once i've got a fleet formed (the fleet has its own control subgroup, usually bind it to key #1 for the main fleet)...once i've got a fleet formed i'll alt+click the fighter squadron icon in that fleets pinned info in the empire tree(on the left-hand side of the screen). this will select every fighter squadron in the fleet automatically. i'll then make a keybinding for those squadrons, usually assign it to key #2 (keyboard shortcut: ctrl+2).
so i've got #1 as the keybinding for the main fleet and #2 as the keybinding for the fighter squadrons belonging to that fleet. if i have bombers i'll similarly assign them to #3.
when in combat i'll generally select the fighter group and then shift+click on targets in the order i want the fighters to attack them in. only have to do this once at the beginning of combat, they'll remember the target order until you give them new orders. its very easy to give them new orders mid-combat as well since they're all bound to just 1 key. when you want to over-ride their previous orders make sure you just regular click, if you shift+click the order goes to the back of the orders queue. a regular click will reset their orders and execute the order you just clicked.
i know alot of people recommend keeping the squadrons on hold-position orders so they spend less time flying around and more time shooting. i've found that its only a marginal increase in firepower (i'm sure people will disagree with me about that statement, but so be it) for a very large sacrifice in survivability. the squadrons are really sitting ducks to Flaks and anti-squadron specials if they're not circling. so i keep my squadrons on grav-well circling orders. they still seem to do more than enough damage and they die much less so i prefer it.
regarding level 3 Flak Burst:
a single l3 Flak burst will deal about 75% damage to TEC fighters. deals about 90% damage to advent fighters and about 45% damage to vasari fighters. (different race's fighter squadrons have about the same number of total HP but its spread around between different numbers of fighters in the squadron). catching a squadron in a Flak burst will severely weaken it and that squadron will probably be picked off in short order by other fighters or flaks frigates. two l3 flak bursts kills basically any number of fighters.
i recommend manually timing the Flak burst (meaning take it off auto-cast). the auto-cast AI has a bad habit of spamming it as soon as even 1 squadron is within range. you should keep an eye on the situation more closely and manually fire it off when a good number of squadrons are within range. its pretty easy to catch 4,5,6+ squadrons with it even in relatively small fleet battles. you just have to wait until they make their attack runs and fire the burst as they come in and attack your ships. this also, of course, requires keeping most of your fleet balled up around the Kol so they can be defended by it.