Originally Posted by WillFam-Reno

When a new pad is installed, or an entire disk brake system is new, the pad is not perfectly aligned with the disk. Single sided brakes push the outside pad against the rotor and causes the rotor to be deflected against the inside pad. This is true of Avid and all single sided disc brakes. Dual sided brakes do not exhibit the same deflection, as both pads are pushed into the rotor.

Any non absolutely flat pad-to-rotor contact will cause only a small amount of the pad to press against the rotor until the pad is worn so that the contact against the rotor is uniform across the entire pad surface. If you observe pad wear, the first few dozen stops will seem to wear the pads out at a much faster rate than the rest of the pad's life. Brake material does not have to be on the rotor, but won't really hurt it either. Friction is friction.

The statement "bed the pad in" is usually used to indicate the pad, when deflected against the rotor, to be parallel, or more accurately, equal pressure applied across the whole face of the pad. Once worn in to this shape, cleaning the rotor will not affect this equal pressure wear. Replace the pads, and initial braking will be severely decreased until the pads are applying equal pressure on the whole surface again.

I have not noticed any gain by having a bit of pad material left on the rotor, but will guarantee a very large decrease in braking power if there is a bit of oil on the pad/rotor. I think this was the point of the OP asking for cleaning suggestions.

I use the alcohol pads and they work well. It is also easy to carry one or two in a repair kit in case the need arises to clean the rotors on the road - like after changing a tire.