Zone 1 will play all sources/inputs, Zone 2/3 will play all analog and internal sources, Zone 4 will only play first 6 HDMI inputs (all but 6&7)
In order for the Zones 2/3 to play DVD audio you will need to connect the DVD analog audio to the SC-69...this will be the same for any HDMI/Digital input
So if you connect a sat receiver up with component video and a digital audio, you will also need to connect the analog audio of it to pass to zones 2/3, and you will net see it in zone 4.
again, zone 4 is a HDMI output only so no other sources will play there except the first 6 HDMI inputs..1-5 + BD. 6&7 wont pass through to zone 4
Not sure how you program a harmony remote for this, may take some tricky programming to do this..don't know harmony that well.