Greg, I assume the game you're talking about is MK2.
If you have a PC that is 1-2 years old or newer (1.5Ghz or faster), then what is the point of having the game in there? MAME emulated MK2 very well on such hardware!
the only game you should consider keeping around together with MAME are games that are difficult to emulate, or are not emulated (e.g. San Fran Rush and any 3DFX game.. these games need 4-5Ghz CPUs to look smooth!)
In their case.. think of the JPAC as a PCB board. So the correct hookup will be:
PC + JPAC --->
Real PCB ---> Jamma harness in your cab (joysticks, buttons, monitor)
You need a way to switch between them (expensive solutions exist) or do it yourself.
Save yourself the time and hastle.. sell the MK2 JAMMA board, and the money you get buy a better PC!