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I would take them off completely and do it right but....
if you are not aware how to do this, you could probably do a pretty good job on the car. Just make sure you use a toothbrush or small brush to clean the surface, then use a high quality paint and you might want to tape up the rotors so you don't get paint all over the place, you also have to make sure you don't get any mist on the fenders.
I used folia-tec caliper paint....it comes with small brush and cleaner. Its easy to paint while on the car. If you jack up car a little extra to get under, you can get at all angles. Good stuff.