-If I'm shooting macro with the SB-200s attached to the lens, I use Macro mode with TTL. I may use 2 or 3 lights depending on the subject. I almost always have AB& in TTL.
For anything else, I use Commander mode and will use TTL or M.
AA is auto aperture.
In commander mode, the flash output-level compensation, is basically letting the flash be set automatically,but telling the system to take that auto setting and adjust it with more or less power. It like using exposure compensation with your camera exposure, only it affects the flash output instead of shutter speed or aperture.