You can use both the HDMI and 5.1 analog outputs at the same time. The Toshiba will not disable the output to the analog side when HDMI is connected. I tried this just a few minutes ago and got a big boost in sound clarity.

Miscanthus, I would suggest simply taking HDMI out from my Toshiba HD DVD player and running it directly into the rear HDMI input on the Samsung plasma display. No need to go to your 990 with an HDMI to DVI cable. The only benefit you would gain by doing this is the capability of using the 990 as a switching unit for your video sources. If this is of importance to you then by all means run the video through the 990. You will have to purchase a second DVI to HDMI cable if you choose to do this. Toshiba HDMI out to 990 DVI in. 990 DVI out to Samsung HDMI in.

If you do not want to use the 990 to switch between your video sources. Then do as I originally suggested. Toshiba HDMI out to Samsung HDMI in. Plain and simple. This will take care of getting the video signal to the display. Also, you will not have to buy a second cable.

Now for the audio side. Simple, 5.1 analog Out from the Toshiba HD DVD to 5.1 analog in on the 990. This option is the best that you can do with this player for right now. This is how I have recently set mine up to play and it sounds way better than this next option.

Audio option 2. Take a fiber optical cable and connect the Toshiba's optical output to the optical input on the 990. That's it. This option works but does not offer the benefit of Dolby Digital Plus. All output is in DTS format ONLY.

I suggest using a 5.1 speaker setup for now. 7.1 output is obviously not supported through the analog outputs, and the optical or digital coax. is not going to support any of the higher audio formats found on HD DVD. The Toshiba transcodes all audio formats to DTS as a default setting when output over an SPDIF connetion like optical or digital coaxial cable. This means 5.1 or at best 6.1 surround sound.

In order to get 7.1 Dolby Digital Plus you will have to use the HDMI output. But, there are no receivers or processor on the market which support HDMI inputs for audio processing as of yet. At least I am unaware of any that do.
This is something for the near future. You will be looking for a processor or receiver which supports a version 1.3 HDMI input on the back panel. To be honest the Toshiba will only support Dolby True HD in a 2 channel format. Furthermore, it does not offer support for any of the Dolby True HD multi-channel (7.1) formats. Also DTS HD is not supported according to the manual. I am still a little fuzzy on the DTS HD as it is not all that clear. Anyway I hope this helps you out a little.