Here's the corresponding part in the schematic:
The connector is oriented as follows, when looking at it from the front on the board
The expansion connector pins are directly brought out from the AM335x SoC. Anything > 3.3V on these pins will permanently damage the board! Also, applying signals before the board has booted to any of these pins will damage the board.
Currently, the muxing on these pins is fixed but future SW revisions will add the ability to configure the pinmux on these pins individually to make them GPIOs or select alternate functionality available on these pins using the "config-pin" utility.
The GPIO and other peripherals can be used the normal way as in any embedded Linux system using the sysfs interface. TODO: Add examples here.