So the CD player is hooked up and working, but the DVD and satellite aren't getting audio or video? Let's walk through the process and make sure all the I's are dotted and T's are crossed.
Connections: Make sure all the cables are connected properly. You've already done this, it sounds like, but it can't hurt to double-check.
DVD setup: In the 990's INPUT SETUP/DVD SETUP screen, make sure the audio input is set to the correct digital input and the video input is set to DVI1.
VIDEO_ setup (whichever video input is being used for the DirecTV satellite box): In the 990's INPUT SETUP/VIDEO_ SETUP (or SATELLITE SETUP, or whatever the name is now if you have modified the input label), make sure the audio input is set to the correct optical input (optical1?) and the video input is set to DVI2.
Satellite receiver setup: Make sure there are no settings in place that would prevent the optical output from working when HDMI is also in use (I've heard of a few sources having trouble with the HDMI output preventing the digital audio output from operating at the same time).
TV setup: Make sure the set is using the DVI input. Then switch between the DVD input and the satellite input (video_) on the 990.
Once you've done that (much of which is probably already done), let us know if you are still missing either audio or video from either the DVD or satellite source.