Like Cruzin said - the worst thing you can possibly do is leave brake dust on your wheels (for even short periods of time). This not only goes for aluminum polished or otherwise), but chrome wheels as well.
The "clear coat" on your wheels can be removed, and then the wheels polished (recommend you not try this yourself) but unless you stay on top of the brake dust, the pitting will come right back.
The scratching likely comes from wiping the brake dust off when dry. Best to dampen the cloth you use with detailer spray and then lightly wipe it off. Follw that with another wipe using a clean side of the cloth.
Brake dust will stay in the cloth, and cause additional scratching - so make sure you always use clean cloths.