No matter how it interfaces with the stereo, your iPod is working hard to deliver sound to your car. To avoid your iPod cutting off in the middle of a "Free Bird" guitar solo or a compelling podcast, make sure you back up the device with an additional power source beyond its own battery.
One option is to use a battery backup accessory. Battery backups allow you to run the iPod on AA batteries but don't last terribly long -- some run out of power after eight hours, while others claim they'll run for 40 hours. After the iPod's power does run out, you can always replace the batteries. But if you plan on using your iPod in the car frequently, it's probably better to invest in a charger that feeds from your car battery.
Most people prefer to take power directly from the car instead of using a backup battery. You can do this easily using a charger that connects through your car's cigarette lighter. These chargers are very common and easy to find in stores or online.