Well the way those 3 pin power connectors usually work is that the center pin is always the unswitched voltage and the other two pins form a switched 'ground connector' which is normally closed when there is no plug inserted into the connector. So usually the battery's positive terminal is wired to the center pin output pin of the boards connector and the battery's negaitive is wired to the normall closed contact or the connector and the common switch connector pin is wired to your board's ground system. So when you plug in an external plug the battery 'loses it's path to your board's ground bus but the external DC source is connected via the connectors positive terminal and common ground pin.
This drawing may help, it's of the pins on a typical board mounted DC power connector. Pin 1 is wired to your battery's positive terminal and also to the boards DC power bus. Pin 2 is wired to your boards ground bus, and pin 3 is wired to the battery's negative terminal only.
That make sense?
Lefty