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I can't seem to make the editor map the pads to be on separate MIDI channels can anyone help me?
Pretty sure MIDI channel assignment is per bank, not per pad. The online editor might not make this obvious, but the BASE II wiki page does say as much. It would be nice if it was more flexible without getting into scripting. But... You could configure a MIDI utility (standalone or in a DAW) to intercept the BASE output and remap designated MIDI note numbers to specific channels.