No. I'm saying that the DVI switching is just a pass-through. Thus, the 990's DVI output only gets a signal from a DVI input - and if a source is selected that uses any analog video input (composite, s-video, or component), the DVI output does not get that signal.
Right. Once you hook a couple sources to the 990's DVI inputs, you go into the 990's setup menu, go to input setup, and set the "Video" input for those sources to their corresponding DVI inputs. Exactly like you select "Comp-DVD", "Comp-Vid1", "Comp-Vid2", "Composite", or "S-Video" now.

The part of this process that you need to keep in mind is that you still need a separate analog video connection to your HDTV. The easiest thing to do is to use a component connection, although depending on the sources that may be using it there are cases where a composite or s-video output will suffice. Let's use an example: I connect a Blu-ray player and an HD cable box to the 990's two DVI inputs (assigning "DVI1" to the DVD and/or 7.1 Direct input for Blu-ray and "DVI2" to Video1 for the cable). Then I connect a Wii and an old DVD recorder to the 990 with component cables and an SMS-1 to the 990 with a composite cable. Now I have to run both DVI (or DVI-to-HDMI) and component cables to my HDTV. I need to select the DVI/HDMI input on the TV when watching the Blu-ray player or HD cable box. Then I need to select the component input when playing the Wii, watching a disc on the DVD recorder, configuring the SMS-1, or looking at the 990's setup menu.