Okay, let me illustrate this for you. On the bottom of your Centipede, you'll see a rectangular metal box with a big transformer, a big blue capacitor, and a bunch of fuses on it. This is the main power supply for your monitor, your coin door lights, your marquee light, and your circuit board. Unless you plan to rewire all of your lighting and monitor power, you should just leave that in there, as well as all the wiring to and from it. Just remove the five fuses in the clips, but the leave the fuse in the round black fuse holder.
Now, this is not a Centipede cab, but it IS a JAMMA cab that I used a Centipede power brick in for the isolation transformer and lighting. Here is what the finished product looks like:
You can see the switching power supply mounted to the right wall. It is getting power from the power brick at the bottom of the cab.
In this next pic, you can see my line cord plugs into the right side of the power brick. The round black fuse holder was missing, so I ran the wires that went to it to a fuse I placed a little farther back. Since this cab did not have any wiring when I got it, I ran one wire to the power switch at the top of the cab and then back down to the fuse. The front connector that has the red heat shrink on it is the power to both the switching power supply and the marquee light.
In this next pic you can see I made a custom connector with only two pins that supply the isolated monitor power. The connector is located in the far back left corner:
This last picture shows the switching power supply. The white, black, and green wires are the power coming from the power brick. The other wires are the +5, +12, and Gnd wires to the JAMMA connector. The single blue wire going over the top (which I haven't stuck in a loom yet) is the +12vdc power I'm using to power my coin door lights:
So - unless you're sticking a $5000 MAME computer in there and need the space, I'd leave the inside original, add the power supply you need for the JAMMA board, remove the five fuses on the left of the power brick to remove unnecessary power to the original harness, and put in your JAMMA harness. Piece of cake...