You're putting that Note message into the Hex Code field of a MIDI Preset, right? If so, you can set the MIDI Device right above the Hex Code field, and set the MIDI Port of the MIDI Device, to control what port the message is sent to.
Note messages are channel-specific, so another approach would be configuring Lightkey to only respond on a specific channel, so it ignores the messages you're sending to the Flow mixer on channel 16.