The backup battery is designed to protect the contents of your device if the main battery goes flat, or when you're swapping batteries. The whole point of it is to remain at 100%, as that gives you most insurance if you do something wrong.
It's usually internal and non-servicable, and will recharge itself, but older Pocket PCs just use a 2032 cell instead.
It provides just enough juice to keep power supplied to the RAM and nothing else. You can't run your Pocket PC from it.