If I understand you well and you're trying to transfer a song you already have recorded:
1st - you should have the Fantom and de Cubase both IN SYNC. If you choose one to be the Master, the other must work as slave. You must do this to prevent tracks to be off sync. It should be not important wich is wich but I would have Cubase as Master since this will be the ... master recording device

. Also, use MTC as this is most commonly used today and should offer some more reliability. Make sure to set both MTC at the same frame rate.
2nd- You can do this track by track, mutting 15 tracks and having just one playing, us D.U. Soul suggests.
Now, if you're talking about MIDI tracks I would record all tracks at once to one track in Cubase as you most probably can split MIDI channels to individual tracks in Cubase. I'm not sure of this in Cubase but I can do it with Sonar. Just check it.
If you're talking about Audio Tracks you must use the track by track method unless you're already satisfied with the mix and don't want to do further editing. If that's the case, just use a stereo audio track in Cubase to record.
3rd - If you're just talking about MIDI tracks consider saving the Song as SMF, then transfer the file to the PC and open it in Cubase.
Hope I clear it up for you guys
