Cable modem was down all day yesterday, so I'm playing a bit of catch-up. We'll knock out one simple one first... The two "mixed" outputs are stereo analog audio that is downmixed from multichannel sources (DVD-A, SACD, Dolby 5.1, DTS) - it is there for older receivers and pre/pros such as your Adcom that lack digital inputs, or for connecting directly to a TV.

DVD-Audio and SACD are both subject so certain copy protection restrictions that other formats (CD, DVD-Video) are not. This means that the manufacturers are limited in how the signal from DVD-Audio and SACD discs can be output. The standard approach is to convert the material to analog inside the player, which requires to you use the 5.1 analog output. There are some exceptions to this - some manufacturers have proprietary encrypted digital connections available (such as Denon's DenonLink, which is available only on their upper-end gear and until recently was only allowed to carry DVD-Audio); both DVD-A and SACD are now allowed to pass over an IEEE-1394 (FireWire or iLink) connection with the proper encryption; and DVD-Audio can be carried by HDMI (SACD should follow in a future iteration of HDMI). All of these exceptions are rare, however, due to the very slow development of an approved digital path for the two formats and the sluggish sales experienced by both formats. If you use the coaxial or optical digital, the player will generate a down-mixed stereo signal (similar to the signal produced for the stereo analog output), negating the benefits of the high resolution audio format.

If you have separate DVD-A and SACD players, you will run into the problem of how to connect both to the single multichannel analog audio input that most receivers and processors offer. There are some multichannel analog audio switching solutions on the market to help with this, but not many.

Why does the 990 offer a 7.1 analog input instead of 5.1? Good question! Currently, there's not anything out there that will generate a 7.1 analog audio output, so you're not likely to need all eight channels. (Some people have been known to use a 7.1 input to feed the surround channels from a DVD-Audio or SACD player to the surround back speakers instead of the side surrounds, but that's a separate issue.) The main reason to include a 7.1 input is future-proofing. At some point in the next year or so, we're going to have two new formats on the market: HD-DVD and Blu-Ray. Both will offer Dolby Digital Plus and DTS-HD audio, and these will be true 7.1 formats. While the specs for how these formats will be output digitally are a bit fuzzy (making it impossible to design a receiver or pre/pro today that can accept a DD+/DTS-HD digital signal), the players are expected to mimic early DVD players by including onboard DD+ and DTS-HD decoders that will output the new audio formats in 7.1 analog. At that point, having a 7.1 analog input will grant you the ability to make full use of the new formats.
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gonk
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