Hang it there. You'll get it. Even though it seems intimidating or a bit confusing at first it really isn't. I mean afterall, some of us have figured it out.
On my cable box, which isn't exactly the same but best I can do as an example, my component cable goes from the cable box to the TV for both video and audio. I picked up a very nice and reasonably priced 5 cable cable from Monoprice (now that's smooth hey?) and run it to the TV. 3 cables for the r/b/g component video and 2 cables red/white for analog audio. When I want to watch Just TV, not listen to the TV through the stereo, the red/white analog cables carry the audio to the TV. Plus I don't really care if the TV is getting a dolby digital signal from the highdef cable box. THEN to my stereo I run a coax digital cable (could be optical as well) that I also bought for a reasonable price at Monoprice to the stereo. So when I want to watch TV and listen through the stereo (like football games yesterday) the receiver gets the digital signal from the cable box, video to the TV via component, and I turn down or turn off the TV's speakers AND doing so keeps the dolby audio information intact to my stereo in a way that using the analog audio ports would not.
It sounds like you need to do something similiar.
And I went through that to say this. IF you use HDMI on some of these sat/cable boxes you will lose the audio signal on some of the other ports. I don't know if yours does or not. Just know that if you go to HDMI, which you can also pick up for a very reasonable price at Monoprice
, you may lose the audio signal.
The audio ports on the back of your SAT being audio 1 or 2 probably don't matter. It probably has the same audio feed to both. Probably the same if you have more than 1 set of composite video ports.
IF you decide to run a setup similiar to mine you will need to configure your Yamaha to use whichever digital port in that you choose an assign it to the input source you also select.