P.S.
In SFC3, it doesn't really matter what hardpoints you use for primary weapons and secondary weapons. I've toyed with settings to have the last 10 as phasers and first 10 for torpedoes, and this was when I was bored.
As long as you properly set the arc for a particular hardpoint, and designate whether a hardpoint is primary or secondary in the defaultcore and defaultloadout files, the game really doesn't care.
Makes for some interesting ships.