Aren't the CD inputs digital? If so, no SACD that way.
What pre-amp are you using? My Sony 999ES has the 5.1 outputs as well as the standard two channel. I never had a reason to use the two channel outputs other than to compare them with the other outputs. The two channel outputs in addition to the 5.1 on multichannel machines is provided for those who have two channel rigs.
My pre-amp (Arcam AVP-700) has a direct mode for both two channel CD and the 5.1's inputs. I compared both outputs on the Sony to both inputs of the Arcam and they sounded identical.
I used to own a Outlaw model-950 pre-processor and the difference between the 5.1 inputs and two channel inputs on it was night a day. The 5.1 was much better. Wider and deeper soundstage, more detail, etc.
I connect all six of the 5.1 channels even though I listen to music in a two channel mode 99.999% of the time. I use my CD inputs for my Naim CD5i. Redbooks on the Naim, SACD's on the Sony.
The 3 cables for front/center/surround are going into the multichannel inputs on my yamaha rxv2500 receiver. with this I'm not getting any treble/bass control or use of the sound fields/subwoofer, etc. Although the signal is more pure, there are certain recordings I would like to tweak. I may just have to hook it up to the CD inputs on this system and see which I like better. It's inside an entertainment cabinet and a real pain to connect and disconnect. thanks for the input!