This is are how the pins are laid out on the board. The numbers in brackets are the actual pin numbers of the microcontroller. Pins IO* are digital and S* are analogue.
If your shield's pins are surface mounted i.e. not going through/below the board then you should remember to mirror the layout above, like so.
You connect a 3.3V regulator to VBAT and GND with a couple of capacitors (depending on the regulator you use) to get a steady 3.3v voltage from the battery.