I'm having a hard time wrapping my head around how this works I think.
The understanding I have now, which I think is wrong, is that I have, say, 12 AP guns. If I had 3 counters of infantry in front of an Ogre I could apply 4 AP to each of them, or 6 to 2 counters etc. as long as I don't fire at a single counter more than the one time. If this is true and I only had one counter of infantry in front of my Ogre could I apply the full 12 AP for the automatic kill?
Not only could you, it would be the only logical thing to do. Since your understanding of how AP against infantry works is correct, you might as well throw everything at it; because if you miss, you can't take a second shot at the same infantry with the APs. You _could_ fire at them with a different weapon (Main battery, secondary, whatever). The "can't fire at the same target" rule applies to AP weapons only.