on a jamma harness I think the first pin on the top side (they should be numbered) is Ground/Common, which is where you want to connect the black wire from power input to the converter. When I did this I just stripped back a little of the insulation of the wire that goes into that pin and soldered to it.
the sixth pin is +12V. Connect the red wire from the power input to this pin.
If you have a multimeter you can confirm this by setting it to voltage test and placing the black probe on the ground pin and the red probe on the sixth pin. This should read about +12V (if you reverse the probes it will read -12V). If you keep the black probe on ground and move the red probe to pins 5,4,3 (don't remember which one) you will find +5V also.
You can also google "Jamma harness pinout" and find some info on exactly what each pin on the harness is for.
I just installed a RGB to NTSC converter yesterday to play jamma boards on a CRT TV, so all this stuff is fresh in my mind..... hope it helps.