It sounds like I should use the 7.1 Direct input with my HD-A1 and let the 990 handle the BM, and speaker distance/levels since I have the speakers set to small. Therefore, I should set the HD-A1 5.1 outputs to all speakers "Large" to bypass the BM.

What should I set the Sub and crossover to on the HD-A1?

BTW I also use the coax connection connected to the DVD input for SD DVD viewing. I will have to compare the sound from the DTS track and the DD+ track on HD DVD.