If your display supports DVI or HDMI, you would want to run the player's HDMI either straight to the display or (if you have a second DVI/HDMI source) through the 990's DVI switching. At the same time, you'll want to make an audio connection to the 990. If you were to use the coaxial or optical input, you would be restricted to Dolby Digital or DTS audio - the 7.1 analog output (or 5.1, in the case of the initial Toshiba HD-DVD players for some odd reason) could be connected to the 7.1 Direct input on the 990 and would allow you to hear the new audio formats (Dolby Digital Plus, DTS-HD, and Dolby TrueHD, although TrueHD is limited to two-channel on the initial HD-DVD players).
If you did decide to use a coax or optical input and haven't got any more inputs available, there are some switch boxes around that could let you use the same digital input on the 990 for two different devices. The DVI and component inputs are video only, however.