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In order to do the mapping you'll have to remove all the ccs (or midi notes) from the preset, load it to the board and do the desired mapping. Then assign the messages you removed from the proper controls, remove the others, load the preset to the board, and do the desired mapping. Then you can assign all the messages back to the controls and you should be good to go.
Really, I think audio software companies need to step up their MIDI mapping game. The current "map to whatever the last message received is" paradigm makes it pretty much impossible for hardware companies to make anything that outputs more than one message from a single sensor/control. CoMA mode is really just a workaround for antiquated mapping schemes.