Just build two combined commands into your choice remote, for switching video on the scaler and for switching audio on the 990.
You only need one video cable from your 990 to the scaler, for displaying the 990 setup, composite is good enough.
One thing- you won't see the volume setting and other 990 popups on your screen anymore, you have to select the 990 video input on the scaler.

If you're using DVI inputs you don't get those overlays anyway.

Cheers,

Actually, you won't get the volume setting and popups with component inputs, either - just composite and s-video.