Only MM1 and the HD channel broadcast in Dolby Digital... and only on some content.
Otherwise, The quality will depend on your AMP's and the Decoder's respective DSPs.
Be sure to change the "Language" of the channel to "Dolby Surround".
I've noticed that content from MM1 and the HD channel that isn't DD, comes through the SPDIF as PCM... this "should" be better quality than normal stereo but again, it comes down to the input bit rate. (providing the AMP is doing the PCM decoding... since the YAMAHA DSPs would be way better than the cheap ones in the DSTV decoder)
With the PCM content, your AMP should pick up the "digital" signal. I'm not very familiar with YAMAHA AMPs, but your display should have a indicator saying that the input is "PCM DIGITAL".
I'm not sure how the SPDIF passthrough works on the DSTV decoders, but I assume the "DSTV decoder" is probably doing the decoding of the "stereo" sound on the other channels. Which is why you're not noticing a difference.
Do yourself a favour and get a proper digital co-ax cable. They're shielded to prevent interference. A normal sub RCA will work but the higher freq's of the digital signal means there should be a "better" insulating layer between the outer layer and the inner core of the co-ax cable.
Usually available at any AV section of electronic stores. Ranging from R150 to R400 for 1.2m
They're a little more expensive, but if your AMP is wired to as many components as mine... you'll know what interference is all about... My DVD co-ax cable used to mess the "component out signals" of the DVD machine into the AMP. I was using a regular RCA cable for the sound. I changed to a proper shielded co-ax cable and the picture went back to normal.
I've got it hooked up and running 100% on my HD PVR. I prefer the co-ax to the optical because the DSP's are different on my AMP. The co-ax DSP issues a lot more bass then the light-pipe DSP so I don't have to crank up my sub... and everything sounds "warmer".
The passthrough works with the PCM stuff and make the "Dolby Pro Logic II" and "DTS Neo6" features of my AMP really come alive.
Otherwise, I enjoy the movies broadcast in Dolby Digital... Hopefully, the digital content increases.