This will be either a 6-pin or 10-pin connector depending on the version you got.  It is directional, so be sure to line up the notch in the connector with the notch lines in the silkscreen on the PCB.  Solder the connector into one board - they're both the same, so it doesn't matter which one.

Using the provided standoffs and screws, screw the two boards together, making sure the notches line up on the same corner. 

Drop the pogos through both boards, their smooth rounded ends should rest against the black connector.  Make sure all pogos are resting at about the same height.  Solder them to both boards, using the extended pads to get a nice fillet to each one.  Flux helps solder flow to the pogos.