Well, an ATX power supply is a switch-mode powerbox, transforming 240V AC into several smaller voltages. Look for the manual online, or find the ATX supply info for pentium 1 boards.
Look up ATX in wikipedia for some basic info on the variations on ATX boxes. To create -V, just swap direction of leads on a battery. 12V=12V above gnd, -12V=12V below gnd, just remember that -V needs -V regulator, ie 7912.
I dont think that using an existing ATX box and battery-packing it is the best approach, rather find the voltages needed and create your own powerbox. I have no idea how fickle a MB is in regard to power consistancy, and have no direct experience making power supplies of this nature, but usually you need clean 12, -12, 5, -5 and 3.3V supplies. There's prob more than a few parts you could scavange from an ATX box, keeping the price down.
hope it all goes well, love seeing junkbots