Supply power to mini-ITX from car battery
Mini-ITX does not standardize a power supply.  If your board takes 12V, then yes, you need a DC-DC converter that converts the battery voltage to 12V.  However, according to Wikipedia, a 20 or 24-pin standard ATX power connector is conventionally used.  

This connector has a number of independent supplies for 3.3V, 5V, and 12V.  Here's the PDF standard if you want to develop your own - It's not trivial! You'll need to know the power requirements of your mini-ITX board to determine how many amps each supply needs to provide.

However, there are a number of ready-made solutions.  If you have an inverter available, a standard ATX power supply will work fine.  mini-box.com has been debugged (good or bad, your choice) on this site before; their m-series power adapters are specifically designed for in-car use.