there are 3 ways to supply the Naomi 1 & 2 motherboards with the voltages they require
1\ a suitable JAMMA > JVS I/O board like the Capcom I/O or the Sega V2 I/O. both of these take the 12v and 5v lines from your regular JAMMA PSU and converts one of the voltages to output at 3.3 aswell as the 5v & 12v from your JAMMA PSU.
2\ Sega Naomi PSU - as found in the Naomi Universal cabinets
3\ a regular ATX PSU
to use a PC PSU you need to identify the voltages needed.
we are looking for +5v, +12v and 3.3v
the pinout for ATX PSU's can be found here
http://pinouts.ru/data/atxpower_pinout.shtml
once these have been identified we then need to know the pinout for the 8 pin and 6 pin connectors on the Naomi motherboard
the pinout can be found here
http://webgb.hp.infoseek.co.jp/gtech/connect.html
although they aren't strictly required, it is also advised that you obtain the correct JST connectors as required by the Naomi motherboards
heres my Naomi PSU adaptor to allow use of a PC PSU

and heres it plugged in to a Shuttle PSU

the 2 pin header is for an on/off switch, just a switch between pin 14 and a ground as you need to short pin 14 to enable the PSU to power up, you can simply just make a wire bridge between a ground and pin 14, I personally use a simple switch.