The problem is that you have so many individual wires that would need to be switched. A standard ATX motherboard connection is 20 individual wires. There's also the 4-pin 12v (if your motherboard utilizes it), molex connectors for drives and so forth.
Your best bet is to take a beefy ATX power supply and hack a molex connector to supply 12v to your DC-DC power supply. Another option is a 12v power supply that will provide enough amperage for your DC-DC power supply.
Or just use a laptop for your car system.