I simply congratulate myself for not writing "blu-tooth setup." Since my TV has HDMI and the player has HDMI why would I need to run it through my pre-pro? If I need to can I use the three-color cables that will run through the pre-pro? (They have some kind of peculiar labeling like Cy Xy and Zy.) So I guess my question(s) are: Why run the cabling through the amp and if I do can I use the three-cable combo? Gonk?

You would only need to run HDMI through the 990 if you had a second HDMI or DVI video source - at which point, the video switching convenience is handy.

The three-color cables are component video (the highest level of analog video). If you use HDMI, there's no point connecting the component video. With Blu-ray and HD-DVD, HDMI will always support the highest resolution. It also allows the video to stay digital all the way to the HDTV, which is a nice approach since a great many HDTV's are digital display devices. There's also a flag that can be set by the studios on individual discs (the ICT, or image constraint token) that can force players to reduce the resolution output via component video to something like 540p (or half the vertical resolution - a fourth of the total pixel count - of the original data). At this point, none of the studios are engaging the ICT on their titles. Hopefully it'll stay that way.

Run HDMI from the player to the TV unless you have some other HDMI/DVI source, in which case you can use the 990 to switch between those HDMI/DVI video sources. If you plan to watch regular DVD's in the Blu-ray player, run a coaxial or optical digital audio cable. Assuming you aren't already using the 7.1 Direct input on the 990, use that for access to the new HD audio formats (Dolby Digital Plus, Dolby TrueHD).