the layers are handled by midikatapult. it sends out the same note/cc (i forget which) for each pad no matter what page - but sends it on a different midi channel. so they're all completely different things to map in traktor.
i don't know much about maschine (sadly ) but i'm sure you could do the same kind of thing by assigning the same note/cc to each pad in each bank, but changing the midi channel for each. tho u don't need to do that - just make sure each pad sends out something different.
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