On a real neo-geo cabinet there's a 'select' button. According to the wiring diagrams I have here in front of me, it connects to pin 26 of the neo-geo motherboard. The question at hand is: what does your JAMMA adapter connect that to? You'll need to look at your wiring harness and see what (if anything) that pin connects to. Follow it from the board outwards to try to determine where it goes.
This pin is a no-connect on JAMMA, so if you plugged the neo-geo board into a JAMMA harness without any kind of adapter, then this line is not connected. I don't know what happens to the sound if you do that, though, because the Neo speakers are wired differently than JAMMA.