There is a song playback option which automatically revoices Midi files to use the "optimal" voice; this might help.

In general I process GM files using the "MidiPlayer" program created and supported by Michael Bedesem, which does a good job of remixing / revoicing GM files to be a better match to the Yamaha sound set. See here for a link to MidiPlayer and other useful stuff: http://www.svpworld.com/psr_software.htm