Is it a Mini-ITX system by any chance? I run one of those as my fileserver. You can get in-car power supplies for those at mini-itx.com, they should run other motherboards as well provided they dont need much power. They must have to deal with quite a quite a lot of EMI from the ignition system so might be better for running off the same battery as your motor, although Id still recommend going for a separate battery if you can.