Hi and welcome to forums! You can safely connect the red wire to the +5v on the power supply along with the JAMMA wiring with the PCB. In my cabinet, I connected the ground that's right next to it for the black wire. Nice and simple and you should see the LED lit on the converter when you turn it on. It doesn't take much power so should not affect voltages.
As an added precaution, you can always use a multimeter to adjust knob on the +5v on the switching power supply, but in this case I think you're fine.
D