The way that passage from the manual reads, I would expect that both outputs would work for the incoming video, but the OSD menu would only be generated for the s-video monitor output. That would suggest that you could monitor the video at both the LCD monitor and the front projector, but only get the menu at the projector.
Question, though. Since the 990 will convert any analog source to component and display the OSD menu on component, is the s-video run to the projector necessary? If you left it disconnected and only used the component video, you should be able to get everything except component inputs on the LCD monitor.