[HELP] Rename tracks help please and help with chapters

[Mapsking]

OK, after messing around with it, I got everything working, except when I tried a new movie, one with two audio tracks (movie audio and commentary), I set both individually, added them the audio queue, they showed correct formatting, in the tags section, I labeled the name for each individually, everything seemed to work beautifully, they show up appropriately, except both tracks are actually the movie audio.  The second track LOOKS like it is there, named correctly, etc., but it actually has the same audio as the first track.  I feel like I am overlooking something, but what am I doing wrong, and/or how do I actually get a source file with multiple streams that play fine individually, to show up as two separate audio streams in the output file?

I also notice the original audio has 5.1 channels, but in Hybrid, it is showing as 2 channels. How do I just set it to copy the original audio, or how would I go about changing it?
Thanks, Mapsking