I think what he means is the difference between setting the aperture on the lens via the aperture ring, and setting the aperture on the camera body, via the switches and dials.
for manual focus cameras, u set the aperture on the lens
for AF cameras, you typically have to disable the aperture ring on the lens by setting it to the smallest aperture. the aperture is then controlled by the settings made via switches and dials on the camera body.