You have the option to set Harmony Control.
In Song Play Mode press Menu, Preferences. At the bottom of the general Setup Tab you can choose Harmony Control source. I leave mine on "Keyboard" because I'm always playing chords that the Voice Processor can recognize. If you are playing single notes then you would need to set it to the track where the main backing instrument is (say Player 1 & 2 Track 2 for instance).