If you connect the board to your laptop, but not to the harness, how many buttons show up in the gamepad properties test window?
- More than 3 per player, it's likely to be CHAMMA since there is no "kick harness" connector on the board for buttons 4-6.
How would they appear if they show up? If the numbers are filled in red??
This shows a gamepad with 13 buttons, none of them pressed.
Each button has a dark red circle with a number in it.
- Press a button, it turns bright red instead of dark red.
Joystick shows up as the crosshairs in the "X Axis / Y Axis" box.
- Press up on the joystick, the crosshairs move to the top of the box.
The number of buttons is set in the gamepad encoder's firmware.
- If you have one "X Axis / Y Axis" box and 3 buttons, it is probably wired as standard JAMMA.
- If you have two "X Axis / Y Axis" boxes and 6 buttons, it is probably wired as standard JAMMA. (two gamepads combined into one)
- If you have one "X Axis / Y Axis" box and 6 buttons, it is probably wired as CHAMMA since the board doesn't have a "kick harness" connector for buttons 4-6.
- If you have two "X Axis / Y Axis" boxes and 12 buttons, it is probably wired as CHAMMA. (two gamepads combined into one)

I'm not sure which is the right way to insert it. I'm guessing the correct way is the way that got activity when pressing arcade control buttons.
Final warning before I do an imitation of Reverend Johnson in Blazing Saddles right after he says, "As your spiritual leader, I implore you to pay heed to this good book and what it has to say!"
STOP GUESSING. 
Once again, the
only correct and safe way is to confirm that
ALL of the wires are going to the right pins before you hook it up and apply power.
IMO the best way to standardize your wiring
and allow you to run a variety of boards is to replace the entire wiring harness with a new JAMMA harness.
- It is a bit of work up front, but it will make things
a lot easier to work with in the long run.
- You have to trace the wires anyways, so you might as well convert the wiring to the JAMMA standard while you're at it.
- It would be more work
and more confusing to trace wires through the harness and then tracing them through an adapter.
-- That two step approach more than doubles the odds that you'll make a serious mistake.

- There are lots more JAMMA boards to choose from than Sega System 16 boards so less custom-built adapters are needed.
-- There is a commercially produced JAMMA harness to Altered Beast PCB adapter. Plug-and-play easy.
- The key in Pin 7 is your friend. It will keep you from connecting the harness upside down.
- You should seriously consider labeling harness and adapter edge connectors to clearly show "Parts Side" and "Solder Side". Some harness sellers include these labels on the female edge connector.

Related post
here with easy to edit documents for any custom adapters you want to build.
- A JAMMA harness to CHAMMA board adapter will probably only need two traces cut.
-- Pins 27 and e are grounds on JAMMA, but P1B6 and P2B6 on CHAMMA.
-- Pins 25, c, 26, and d may also need to be cut since they are P1B4, P2B4, P1B5, and P2B5 on CHAMMA.
Scott