In Global settings, I think you set it to Multi, and then the "Midi Channel" selection selects a channel for Layer A, let's say you chose #5, Layer B will then be on the succeeding channel, in this case #6. If you set "MIDI mode" to CC, not NRPN, it should be as simple as sending CC#7 to control volume on each Layer, on their respective channel.
Not completely sure, as I never set mine up like this, but off the top of my head that should be it.