Sins is limited to a max of three weapons per entity.
The actual line that targets fighters is: CanFireAtFighter TRUE
1) To start with a capital ship only having two weapons, copy the Weapon and sub WeaponEffects from the AntiFighter frigate to the selected capital ship.
2) Increase the number of weapons to 3.
3) Open the mesh file for the selected capital ship and copy the mesh points you want to fire the flak from (Weapon-1 or Weapon-2) to Weapon-3.
4) Increase the NumPoints by however many weapon points you copied.
My suggestion is get it working before you start tweaking values. If I missed anything I'm sure someone else will point it out.
Edit- I had this open apparently while Syneptus responded.