"does all of the dvd audio get processed and sent out through the right and left analog or only through the 6 channel analog"
This is set up through the menus. I sold mine a while back so I'm going from memory, but if you dig through the manual the info is in there.
When I had this player most discs contained the audio in several formats, typically a 2 channel mix at a higher sample frequency and a surround mix at a lower frequency. You had to choose which you wanted from the menus. I too only had a 2 channel system, so I chose the higher resolution 2 channel mix and and, to the best of my recollection, was fed only to the analog outputs.
If you use the 6 channel mix and turn off the unused channels, I think it won't sound right because it was mixed for surround and you would be losing that information. It is also lower resolution.. Most of my discs had the stereo mix but a few were 6 channel only and they didn't sound right when I tried to play them 2 channel.