Set to Av Mode
ISO Safety shift = ON
Set aperture to say, f/6.3
Set Min shutter speed to 1/500
ISO = AUTO
Safety shift is not necessary with Auto ISO. In AV or TV mode, Safety shift is protection when you're using a fixed ISO. It's used to allow you to keep your ISO and noise low (as opposed to Auto ISO), but still offer exposure protection.
Hmmm. The above is how I shoot auto ISO AND EC at the same time.
ISO Safety shift only works for a fixed ISO. When you're shooting with the above settings and EC and the light is limited, then the EC is increasing the Auto ISO, up or down. The safety shift isn't doing anything.
However, lets say that you use your above settings; AV: f/6.3, Min. SS 1/500sec, but with a fixed ISO of 400 in order to keep your ISO and noise levels as low as possible, and then the light on the field starts to decrease, then once your Shutter-speed bottoms out to 1/500sec, then the ISO safety shift will kick in and raise your Fixed ISO from 400 to 640 or 800, or as high as is necessary to get the proper exposure.
Does that make sense?