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first you need to connect qtractor midi out to your outboard synth midi input--i guess you have this setup working--then getting your synth audio output into some line-in of your soundcard and then recording it into an audio track would be my suggestion.

1. get midi played by qtractor be sent to synth:
   qtractor (midi track -> midi out bus) --(alsa_midi)--> m-audio fast track pro (midi out) --> yamaha s90es (midi in)
2. get audio played by synth recorded into qtractor:
   yamaha s90es (audio out) --> m-audio fast track pro (audio in) --(jack_audio:capture)--> qtractor (audio in bus -> audio track)

hth.
seeya