It's possible the pin carries two. Look at the auxiliary input with the RCA connecters (red and white). Both are routed through only one pin. My guess is that the headphone is a similar case. It may carry a SPDIF signal, which can hold two uncompressed audio channels. There's probably a separate DAC on the drive bay similar to the console that came with the X-Fi Elite Pro. The only thing that puzzles me is that there are four SPDIF outputs and only one input... which does not match up with the drive bay configuration. I can assume the coaxial and optical SPDIF inputs share the same pin. Even if the two SPDIF outputs do not share a pin, that leaves one SPDIF output pin unaccounted for. The pinout is very vague with its description, but the forum link from my last post had people replying that headphones worked. You should probably read that thread carefully.
If you don't mind me asking, what exactly are you trying to do? Are you trying to connect the sound card to the headphone and microphone ports on your computer case?
