If the source doesn't have both component and composite active, nothing will work (short of stepping component down to composite, which is a potentially tricky proposition since component can cover a wide array of resolutions).

I'm not entirely sure how the 990's switching works for composite and s-video inputs when a component or DVI connection is selected, but I know they aren't ignored outright - the Video 1 record outputs still receive the composite and s-video signals (if any exist), and the second zone can also be used. If nothing else, you could use that second zone capability when you want the small display active (turn zone 2 to that source), but that still depends on the source device actually outputting video via composite or s-video. Also, I'd standardize on one connection for every source being piped to the small display (composite presumably) because s-video to composite transcoding may not apply in all of these cases.