Wow! I was just reading up on the MO6's DAW integration and it sounds pretty darned cool. The keyboard has USB ports plus a S/P DIF digital output so I would definitely look into getting an audio interface that supports S/P DIF. According to the Yamaha site once you've linked up with USB & S/P DIF the keyboard integrates into Cubase just like a VST plugin. Sounds very cool.
With this arrangement you might not even have to record an audio track. You might just be able to drive the MO6 with the midi track and then use Cubase's File > Export > Audio mixdown menu option to generate your wav file.
Check out
Motifator.com - Official website for the Yamaha Motif Family. It's a website dedicated to the use of the Yamaha Motif line. I learned a lot there when I go my old S90.