Caeyk,
First of all, if you get mud flaps, the molded ones look and fit better (I have both types). Now you can paint them. But, remember even hard rubber bends. You'll need to sray with a flex coat on first. However, what I have done with my last two PTs is, just use an adhesion promoter, and paint "PT Cruiser" lettering to match the body color.
Mirrors have the same paint bonding issue. But, again what I have done is get the plastic mirror covers. They are much easier to paint.
