With regards to the first question about how the channels are “ordered”, it’s random. Rather, it starts from a random seed and starts reconstructing stuff, so there’s nothing to “sort” the results. Similarly, if you run an NMF on the same file over and over, the results will be in different places (and slightly different too).
What I’ve done in the past is then run some descriptor stuff on the results and order them either by loudness or centroid or whatever you think is important. @jamesbradbury whipped up a thing ages ago that then takes the weakest results and combine them.
As to the stereo/mono stuff, I think there’s a tab in the help file that explains that, though when I’ve done that I tend to just split things and manage it independently.