Assuming that each fighter only has 1 fire control you are going to end up with each fighter targeting 1 fac.  If there are more fighters than targets then the extra fighters will not have a target to start with.  After the missiles hit the targets the rest of the fighters will be able to target what is left.  This is assuming that the fighter missiles are doing enough damage to cripple or kill a target.  If they aren't getting that much then the multiple target setup is not going to be much help.  I have not used this is a while with missile fighters so there might be something that I am forgetting.  You might also be able to fire a salvo of missiles and then have the fighters that did not fire retarget and fire on the next round (assuming good training levels, otherwise it might be a little longer).  If you think that your fighters are carrying to many missiles for a single target you might want to restrict them to fewer than the full load of missiles and have them fire the rest on the next time around.  If your missiles have any self guiding capability this would work fairly well even if the original target was destroyed. 

Brian

and then you have to re-assign each time a target dies.

try doing that when fighting the swarm.

On the F8 combat screen to the far left there is a button "Same Loc" in an area titled multiple targets.  It was specifically designed to help with swarm combat.  Select a ship and set up the fire control for it.  Select a target for one of the fire control and then use this button.  It automatically targets the same fire control on all other ships of the same class on a different target that is at the same location as the first target and is of the same class as the first target.  If a enemy is already designated as a target it won't be targeted again.  Essentially this means you only need to target 1 ship in each class that is engaged.  It helps quite a lot when fighting large groups like the swarm.  It helps if you assign enough firepower to the fire control to kill a target fairly quickly. 

Brian

Auto fire is for NPR/spoilers. Never use it as a human, as even though sometimes it works, it's never as good as doing it by hand yourself - ie, wasting missiles, targeting less dangerous enemies and so on. To reduce micro, use the "copy assignment to TG" and "copy target to TG" buttons.

I've had problems getting missile fighters to autofire. beam fighters seemed fine but missile fighters on autofire just sat there and did nothing.

Yes they do have the inexperience delay: Striker is preparing to fire but her weapons are not yet ready. But then the message changes to: ASM FC is targeting FAC at 540k km. My bombers does not have search sensors, only fire control, but my gauss fighters are equipped with active search sensors. Maybe that is the problem? I thought that my bombers will be able to fire when target is in range of my other ships active sensors. Do they need their own active search sensor?

Well they were at 540k km, that is 540000 km right?

This FC should be able to get them at that range:

Active Sensor Strength: 28   Sensitivity Modifier: 140%
Sensor Size: 1 HS    Sensor HTK: 1
Resolution: 60    Maximum Range vs 3000 ton object (or larger): 91 080 000 km
Range vs 1000 ton object: 10 120 000 km
Range vs 250 ton object: 632 500 km
Chance of destruction by electronic damage: 100%
Cost: 28    Crew: 2
Materials Required: 0x Duranium  28x Uridium

Development Cost for Project: 280RP

I did not receive any message about ECM, so I don't think that those FACs had any.

It really was initiative problem, thanks for the advice. But I still do not understand why my missile fighters did not open fire.

Unfortunately my fighters are for some reason unable to get closer than 40k km. I gave them order to follow target.

But still my missile fighters should be able to engage those FACs right? Their FC has Range vs 1000 ton object: 10 120 000 km.