So yeah, the way it works is that each incoming MIDI note is assigned to one of the many Misha functions available, shown on page 44 of the user guide. They are all treated the same – so you could assign “+3” to a particular MIDI note, or you could assign a particular chord, say.
Regarding chords, you turn the chord off by assigning the chord name “Off” and triggering that. (You can also assign a MIDI note to trigger stepping one up or down from the last chord selected; or a random chord.)
Not out of the question to add a second MIDI channel for control, but I’m not clear exactly what you are hoping to achieve here. Are you interested in ‘passing through’ some MIDI notes? Even if so, it seems to me in, say, SirParcival’s map, you use three octaves for Misha functions and still have plenty of other MIDI notes available. I realize on a drum kit you don’t have nearly that number of MIDI Notes available, but on the other hand you can get to the entire range of MIDI with one pad, so I’m not sure what it is you want here.
Also regarding standard note mappings – not quite sure what you are saying. Can you elaborate?
MIDI over USB is definitely on our list to add.