In order to keep my shutter speed fast (for my 400mm lens without IS) and an F-stop a little less than wide open for a greater depth of field, I need to set the camera to manual. With those two settings fixed, in order to adjust the exposure, I need to manually adjust the ISO.
With auto-ISO enabled, the Manual camera setting isn't really fully manual. It would be great if the camera allowed exposure compensation for the "not quite manual" setting where shutter and f/stop were fixed but ISO was automatic. [BTW, let me know if this is already a feature and I missed it somehow.]
That's assuming we get the high end ISO performance we're (at least I'm) hoping for. My basic process with my 7D is set the iso as high as I can stand it (which is usually 400, maybe 800 in a pinch) and then just use
Av or Tv, depending on whether I think dof or shutter speed is more important.