I would do 6 channel direct for all sources unless the soundcard is already doing some sort of pseudo-surround for stereo surround already... then I'd do stereo during music.
For games and movies, 6 channel direct is the way to get true surround sound (as long as your soundcard is set up to output 5.1 analog correcty).
For music, it's going to be your personal preference. Playing it back as 2.1 (stereo or 6 channel direct) will play it back without the z-5500s altering it. You may prefer stereox2 or PLII music with the z-5500s altering the sound to give you fake surround.