Single slot motherboards ARE Jamma, multislot motherboards are MVS pinout.
I am currently in the process of hooking up a six slot board in my JAMMA cabinet (while still maintaining the ability to plug and play with normal JAMMA boards as well).
Here is what I have to do.
Cabinet ALREADY has the 4 button JAMMA/Neo Geo layout. So no changes there.
MVS requires at least one of the JAMMA "5th button" to be populated as a game select button. My machine has the 5th button wires on the harness, but they terminate inside a molex connector. So I need to extend the wiring of one of them so it goes all the way up to the panel, then drill and install a game select button.
The audio is the tricky part. MVS grounds its audio to cabinet ground (almost no other boards do this, many can be damaged by being plugged into a cabinet wired this way).
My cabinet currently has two speakers, wired as a single one (Mono).
My solution is to first slightly mod the MVS board itself. I will cut the traces for left channel+ and right channel+ before the edge connector meets the harness. I'll cut them towards the board side of the edge connector so I can always undo it with 5 seconds worth of soldering. Then I will run the wires for left+ and right+ off the boardset itself.
Now for my speakers. First I unhook the original 2 speakers. I install a 3rd speaker and hook THAT up to the JAMMA wiring that had previously gone to the pair of speakers. The original two speakers will get wired to the MVS board. This will give me both a stereo and a MONO setup in a single cabinet.
MVS board is a six slot, large and heavy, it will be permanently installed in the machine, and the stereo speakers will always be connected to it. I will also install a PCB shelf for JAMMA boards as well. Switching to the jamma board will merely be a matter of moving the harness over to the JAMMA board.
There is also another option (which I did not select), and that is making an adaptor from MVS to JAMMA. Or you can cut traces and solder wires and actually make the MVS board itself JAMMA. Either solution will only get you MONO audio. I did not do this because I have a 4 board multi-jamma setup that I am going to eventually install and you CANNOT mix MVS audio and Jamma audio in that setup because MVS audio grounds the negative terminal of the speaker (No big deal for an MVS board, but BAAAAAAD for a JAMMA board).