Tony, don't know where you have been reading that hdmi on a motherboard is only 2 channel, but afaik thats absolute rubbish.. even cheap motherboards have
VIA VT2021 codec
High Definition Audio
2/4/5.1/7.1-channel
Support for S/PDIF Out
What mother board do you have?
Have you installed the gfx and audio drivers for your pc and enabled HD audio? I have had some old pc's that pass the DD/DTS through etc from HDMI, and is not stereo!!
Can you take a picture of the rear of your amp with every thing connected inc speakers.
If the options are greyed out then its either conflicting with an other setting or its not detecting it plugged in if thats a feature of the amp.
do you have one simple player of any kind with hdmi and optical/coax audio on it?
I would do a hard reset on the amp, un-connect every thing inc speakers, do not use the set up mic for now..
Plug say you rear speakers in first then connect what ever you have with HDMI and make it play some music or what ever and change the settings until you get sound from the rear speaker, then start plugging front in etc.
Difficult to do things sat behind a pc... and your to far to come sort it for you..