I have been experimenting recently using an Arduino and an app called Hairless MIDI for creating my own midi device.
It seems like BetterTouchTool cannot differentiate between different Midi Channels?
A MIDI message usually consists of the following three things:
Channel, Note and Velocity
The MIDI viewer doesn't show the channel.
Anyways, the app is absolutely amazing! I can finally stop dreaming about all the things I could do with a custom Midi controller and start doing them now, great 
ah true,I need to add support to access the channel. I'll look into that soon!
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You're an absolute hero! Seriously didn't expect an answer this quickly 
I am using a workaround for the time being (simply sending different Notes instead of using separate channels) - works fine too!
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MIDI channel support would be appreciated by me, too - my Arturia BeatStep allows to switch between 16 channels by simply pressing two buttons simustanely, and show the active channel using only one button. MIDI channel support would allow me to easily and transparent to switch between 16 command sets.
i'd like to chime in and add my support for this. i have several layouts in lemur which i use to control different apps. they all send midi notes, but on different channels specific to the layout. some of those messages go straight to the app concerned, but others go via BTT. any command that shares the same midi note is being triggered by the app and by BTT (which does something completely different.) i have to keep turning BTT on and off, as "disable BTT for...." from the tray icon doesn't work and neither does "disable better touch tool completely" in config