Not sure what the question is re moving things in the channel box?????/
as for 'order of operations' (similar to max's stack) the blendshape node works best if it is running before the skinning node. You can change it's order afterwards by right clicking on mesh and (from dropdown menu) picking complete list. This is similar to max's stack>use middle mouse button to shift the order of things. Can sometimes be a bit tricky at first, but is simple enough.
Double morphing, happens in every program (that i'm aware of). be mindful of which blendshapes are being driven by which bones rotation. eg. elbow morph>elbow z rotate>shoulder morph>shoulder x rotate, clavicle morph> clavicle y rotate.
I found that each (fully extended muslce postition) ie. arm up>arm down is enough to get decent deformation, and since each joint usually only has 2 extremes on each rotation this should work fine.
Any way hope this helps
Mayan elder......only in years.....