Using an xxx-in-1 board in a scratch-build isn't always the way to go, particularly in a Bar-Top. You will need a lot of space for all the wiring and components plus will have to JAMMA wire from scratch so unless you're handy with a soldering iron then you may want to reconsider as the thing could end up quite large.
With specific regards your question; this will depend on the game in question - if it's a 'turn-based' 2-player game, it should be set up to just use a single set of controls, whilst simultaneous games should be set to respond to 2 sets of controls - any xxx-in-1 PCB that's done correctly will be set for this, though there's so many around now it's anyone's guess. Personally I'm not a fan as they're just not as versatile as a PC, many have either sound or graphics glitches caused by their computer brain not being adequate and then of course there's configurability, which is always better with a programmable control interface.