According to the datasheet, your processor has an absolute maximum operating voltage of 6 volts. Giving it 12 volts will do it no favours. How will you separate the USB power from your 12 volt power supply? Again, accidentally feeding 12 volts back up your USB cable will do your computer no favours.
Yeah I figured it might be a bad idea, thanks for the replies.Applying 12v to the VIN pin has always worked before, is it not supposed to? I thought I read the VIN can accept anything up to like 14 or 20v somewhere. I've used 12v to power the arduino micros many times before without issues.