Here's something I haven't figured out yet. I spent several hours drawing this very detailed technical schematic to assist with my inquiry:

Let's say I'm captaining the ISS Slightly Lopsided Isosceles Triangle here. I've got 3 weapons. A and B are plain old regular shooty guns, whereas C is a PD-type weapon. Let's also assume that all weapons are part of a single group, which is set to autofire.
Suppose only Enemy Box Ship 1 is present (I.E. ignore 2 and 3). I know that Enemy Box Ship 1 is in the firing arc for both A and B, so both will target it. But what if, instead, Enemy Box Ships 2 and 3 are attacking and 1 is not there. Each ship is in a firing arc, but they are in different arcs. Will each weapon fire on the ship in it's arc, or will both weapons try to train onto one ship at a time (and thus only one will be able to fire?). And in both cases, will PD weapon C fire on incoming missiles in another arc?
Given that we only have 5 weapon groups to deal with, how to best assign weapons to groups depends a lot on how the autofire mechanics work. An admittedly cursory search through the forums and manual didn't turn up an answer, so I figured might as well ask.