Is Crewchief is a separate program that you are mapping to your headphones and then have the rest of the audio going to your 5.1 system?
Yes, separate program. It has settings in it for where its audio goes.
... PC configured as 5.1 with Optical ...
5.1 optical only works when encoded as DD or DTS. Otherwise you tend to only get stereo - check what your amp says it's getting! HDMI might work in some cases/setups, apparently. I gave up trying to get digital working and went to using the analogue connections.