In your setup sequence on the Sony, you should be able to program that sixth speaker out of the equation. The receiver will then properly decode and process the DD and DTS signal to your five speakers.
When I set it to auto, I only get the front channels regardless of my input, none of which is digital yet, so I just need to pick what sound right and the amp will direct everything to the speakers that I have installed and set up...I did the auto calibrate and it only shows the 5 speakers when I have any of the Pro Logic or Neo:6 set. Also if I get to close w/ the neo:6 there are strange noises coming out of the R & L speakers in the front...is that the matrix trying to add more than is there and when the sound blends with the center and the other front speaker it comes together?
In the absence of a multichannel digital input signal the receiver will automatically output stereo when presented with a stereo signal. When switched to a digital surround simulation format, such as Dolby Pro Logic II or DTS Neo:6, then you will get some sound out of all speakers. You may prefer one or the other. If you hook a DVD player up to the Sony, you will want to feed the digital audio up to the receiver via coax or optical cable. Then the "auto" mode on your receiver will recognize and decode the surround signal on the DVD and feed all 5 speakers according to the demands of the program content.
Why you are hearing strange noises on Neo:6 is a mystery. Shouldn't be happening. I take it that this doesn't happen on DPL II? It wouldn't bother me too much as I've never been a big fan of Neo:6 anyway. I prefer DPL II (Music) mode for all my non digital audio inputs.