The Harmony should be able to provide the macros necessary to switch both the 990 and the VP with a single button. The DVDO units all have discrete input selection commands on their remotes.

As for the wiring, I think you've got it correct: run audio from each source to the 990 (digital audio for sources like DVD or HD cable/satellite, or analog if the source doesn't offer a digital output) and run video from each source to the scaler (either HDMI/DVI for sources that offer it or component, s-video, or composite if that's all that's available from that source).

Talking about macros got me thinking... A video scaler that could integrate with the 990 via RS232 and switch automatically would be pretty slick...