There are a couple possible options. One is to use a switcher to connect the multichannel analog outputs from two players (one Blu-ray, one HD-DVD) to the 990.
This box will let you connect up to three 5.1 sources to the 990 (it's not marketed for this purpose, but it'll work).
This will require you to get two players with multichannel analog outputs, though - which means that you'll be looking at an HD-XA2 or XA3 for HD-DVD as well as a standalone Blu-ray player. That's going to get pricey. I was going to suggest that you consider LG's upcoming combo player (the BH200) which will cost $1000, but it's not going to have multichannel analog output. At the moment, pre/pros haven't yet picked up fill HDMI support, but the players are still getting up to speed (particularly Blu-ray, which is still offering just profile 1.0 rather than profile 1.1 or profile 2.0). If you plan to buy into both formats right now, you might get an HD-A2 or HD-A3 and a Blu-ray player with multichannel analog outputs. The HD-A2/3 would decode TrueHD and then re-encode as high-bitrate DTS (which actually sounds
quite good), and the Blu-ray could use the multichannel analog input. Then once a good combo player that supports profile 1.1 or 2.0 and has multichannel analog output arrives, you could replace both players with that.