Brad225
I don't know that I'm fully understanding your problem but two items that might be of use are:
1. Since I never hook anything up through the front inputs of the 990, I designated my HDTV tuner as Vid5, assigned its optical input and component input, which I do switch through the 990, and run my DVI connection directly to my front projector.
2. Before I ordered the 600, I was very concerned that there were no programmable remotes with jog/shuttle dials. When I got the unit, I was amazed to find that the directional segments of the thumbstick are capable of learning repeating commands; jogging is now a one handed operation, rather than a two handed one.