As to preventing scratches, be VERY cautious as to what cloth you use to clean/polish. Test any clothes out on a very inconspicuous area first just to make sure. Oh, and be careful about most microfiber cloths, since they are microscopic strands of polymer that basically scratch the surface, which is the reason they clean so well.
As to hiding scratches, I have had very good results with Eagle One Nano Wax. The black areas of my bike are the only parts that show scratches and this stuff works very well, especially on the really tiny swirl-mark scratches.