Just think of your PC as a non JAMMA PCB. To connect it to a JAMMA cab you need a converter. The J-PAC is your converter, it ensures all the right connections from your PC go to the right pins in the JAMMA edge connector in your cab.
To switch from J-PAC to JAMMA PCB just power off the cab, unplug the J-PAC, plug in your JAMMA PCB and power back up again.
The hardest part is figuring where in the cab you're going to put everything AND be able to access it all easily.