Not only is it the 990 limiting you, it is the copy protection inherent in the HDMI standard holding you back - a receiver or surround processor can't take a DVI or HDMI input and output an analog video signal. To use the 990's component switching, you
must run component from the DVD player to the 990.
Now, you could run HDMI from the DVD player to the projector and also have component from the 990 to the projector for the other sources. You'd just need to change the projector's input when you watch DVD's.
The audio formats you mention (Dolby EX, PLIIx, DTS ES, and NEO:6) are completely unrelated to the video connection you make. The digital audio cable (coaxial or optical, doesn't matter which) passes the data from DVD to 990, and the surround modes available to you depend on the audio format being played. For example, Dolby Digital 5.1 (what most movies use) would offer the choices Dolby Digital, Dolby Digital + Pro Logic IIx (either Music or Movie), and Dolby Digital EX. A Dolby EX source that includes the EX flag will force the processor to use Dolby EX, and if you change the mode manually to Dolby Digital or Dolby + Pro Logic IIx it will change back if you do anything to interrupt the bitstream (skip chapters, go into and back out of the menu, ...). With a DTS 5.1 track, you can use DTS, DTS+NEO:6, or DTS+Pro Logic IIx (again, Movie or Music). I've got a lot of information on this both
here and
here (with a lot of repetition between the two). All of this assumes that you are delivering the raw bitstream from the DVD, which you probably are. It is possible to have your player set to convert everything to PCM, though, which is
not what you want to do.