Basic cable management is exactly what you describe - keeping power cables away from interconnects and speaker cables (particularly on parallel runs; power and interconnect can cross at right angles and not give you problems). It's also not a bad idea to avoid bundling interconnects with speaker cables if you can avoid it. Tying cables up with string, zip ties, or velcro straps won't hurt them, assuming you aren't bundling interconnects and power cables of course.

So we've got audio and video working fine from the DVD, but we've lost audio and video from the DirecTV? I assume you've started using the 990's DVI switching, so that the DVD player has an HDMI-to-DVI cable and a coaxial or optical cable running to the 990 and a DVI cable is running to the projector? If so, you also need an HDMI-to-DVI cable and a coaxial or optical cable running from the DirecTV box to the 990, and you need to set up an input on the 990 to use that DVI input and digital audio input.