The "auto" light only comes on for full automatic mode. If you press, for example, the A/C button to turn off the compressor, then only that goes to manual mode. Fan speed and output settings are still auto. If you want everything automatic but want to direct air only to your feet, press that button, the Auto light will go off, but fan speed is still adjusted automatically.
Personally, I have A/C set to "remember last setting" and I have it on all three outputs (feet, face, windshield). I used to have it on face only, but it would go full blast on my face when starting the car. Directing the air everywhere reduces the air to your face. Fan speed is automatic.