As norton stated, it depends on the game.
I working on a trackball controller for my Golden Tee 2k and Golden Tee Classic boards using an Imperial trackball. It works great, but I still need to finish the overlay (lexan) and paint it:
I bought the official panel, but it's too big to sit on my lap hehe.
For GT, the wiring for the trackball itself connects directly to the mobo, not to the edge connector. The only wiring to the harness was for the start button and the turn left & turn right buttons. Obviously I'd need to add the additional buttons for the newer GT's...
I built my supergun using the sc200 PSU, which isn't enough juice for the GT boards. Instead, I mounted my GT boards in PC cases and wired the controls to a DB25 connector. I really like this setup - nice and clean. I'd post pics, but it's temporarily sitting in storage. If you end up doing something similar, I can pick it up and take some pics.
Again, for GT you'd probably wire up the trackball much like you would a kick harness: the extra trackball connector would just run to the connector on the mobo. I'm not sure if Centipede uses the same setup...
Let me know if I can provide any additional information.