Capacitor Sizing

Ahhh - what if I have a 5V (3xAA) battery setup on the 5V side, and also have the 12V to the VIN pin ?
So when the car is on, 12V feeds in, the onboard voltage regulator reduces that to 5V for normal running.
Then, the battery on the 5V pin would backfeed power when VIN is lost causing the chip to keep running and remove the voltage regulator burning down the power ? Isn't that a No-NO as the 5V pin supplies curreny

If I left the car battery hooked up, it'd discharge at too high of a rate for my liking. But then, if I use batteries they'll eventually discharge (though using power off with an interrupt tied to ignition would help).
I'm also thinking: How do car manufacturers do it? They have heaps of crap running that probably utilises 5V.. Clocks, radios, etc. - Voltage regulator to reduce to 5V - but then these continually waste power through the drop.