By default, Harmonizr uses MIDI input to select key centers. This way, if you're playing a song and accompanying yourself on the keyboard, harmony will be generated in the correct key.
It is also possible to enable MIDI voices. Just tap the Midi button, and in addition to the automatic voices, Harmonizr will pitch-shift your voice onto every note you play. You can turn off auto-harmony by selecting a single voice in the inversion panel.
Autotune operates on only one voice - your own. Depending on how the preset is configured, pitches can be constrained to just the chord, just the scale, or tuned to the full chromatic scale. Since the other voices are tuned perfectly anyway, you may find you have less need for this than you think.