Ok, so figuring out which pin on the motherboard is the right one is easy. Both pins are small resistances to ground (one is 6 Ohm, the other 9 Ohm), but only one (call it "signal") boots the computer when its shorted to chassis. The other does nothing, so call it "ground." Fine, good.
Now, on the M2-ATX, the connector on the cable is asymmetric: the bottom J8 pin goes to RED, the top pin to BLACK. Otherwise the pins are identical: Both are 3 Ohms to ground in forward bias and Open to ground in reverse (e.g. a diode), and Open to each other in both directions. So I assume the top J8 pin (RED wire) goes to the signal pin on the motherboard, and the other J8 pin (bottom, black wire) goes to the ground pin on the motherboard. I think only this way makes sense though I'd like some confirmation from mini-box or someone else who knows more than I do.
I mean I could hook the thing up, turn on the 12V to the ACC signal and watch what the M2-ATX J8 pins do with a voltmeter... but that's such a pain to set up I guess I'll do it anyway just to be dead-certian.