(1) OK, are you aware that MIDI is not audio? Not being a smart ass, just a front-end question...
(2) Your KC needs a MIDI cable in its MIDI Out port and that MIDI cable needs to go to your MOTU's MIDI In port.
(3) Your MIDI track in your song (no matter what sequencer you are using) needs to have the MOTU's MIDI In as its input to record it...
(4) Once your MIDI keystrokes are recorded from your KC (into the MIDI track mentioned in #3 above) I assume you wish to send it back from your computer/sequencer to your KC and then tweak away, yes?
Is this the case???
Don't fret, it will all work out, just be patient and persistent...
-Alex