Not sure if this can help anyone, but here's what I've discovered:
1. On my Yamaha, the "6-Channel Input" basically overrides the current selection. It's not really on the same level as other source selections. Example, the receiver can be set to CD, DVD, or anything else and when you select "6-Ch Input", this setting doesn't change, but it is overridden with the 6-Ch Inputs. (I hope this makes sense!!)
2. Each input on the Yamaha can have it's own "speaker level" settings.
3. The Harmony, by default, will switch to "DVD" source, then turn on "6-Ch Input". Therefore, all speaker levels will be set to the DVD settings.
Well, after a month of tweaking, I could never get the analog inputs (the sub especially) to be to my satisfaction. The sub was always too low. I would use the remote to the bump up the sub levels by 3-4 db.
But after I realized that the sub levels for each input would be remembered, I decided to have the Harmony switch to another unused input (I used "MD" in this case), then switch to "6-Ch Input". Now I can set the speaker levels of the "MD" inputs to accomodate my DVD-A player.
Rant: WHY DON'T THEY PUT STUFF LIKE THIS IN THE MANUAL!!!!
Anyways, hope this helps someone.