The top two connections on the BBB expansion header we are using (P8) are both GND. The three outputs to control the brightness of the red, green and blue channels are connected to sockets P8_13, P8_19 and P9_14 of the BBB.
The pins are numbered left to right, 1, 2 then on the next row down 3,4 etc. You can also use the pin P9_16 for PWM output.
You can find out about all the pins available on the P8 and P9 connecters down each side of the BBB here: http://stuffwemade.net/hwio/beaglebone-pin-reference/