All you have to do is right click the weapon's in the HUD in quick succession. If you do it fast enough you'll be able to get 2 to 4 weapons on each for/aft facing lit up with the green auto-fire box. I personally am able to get 3 per side.
Some tips if you're having troubles - first, I have to move my Hud window for the weapons layout closer to the middle of the screen (while i'm setting them, then back to normal position afterwords), as for whatever reason I can click faster there then when the layout is at the bottom of the screen. Second thing to note - it doesn't matter if you're trying to 3 out 4 weapons and get a torpedo auto-fired vs. an energy weapon, as that slot, and not the weapon, will still remain auto-fire, even if you take the weapon out of that slot altogether. Finally, you may want to temporarily increase the hud size (esc->options->[hud/layout, iirc]->hud size, irrc). I increased it to max when trying to get all 4 weaps set to auto, and the window positions go back to where you have 'em previously after you change it back to 1.0 (or whatever you had it at.)
Hope this helps, as I much more enjoy the game when I can devote my full attention to positioning and cooldown usage, vs. having to remember to press a fricken button every 2 seconds (gogo q torps at once per 8 seconds)