After a Free Nipple Graft your nipple color may appear lighter then they were previous to your surgery. This is normal, because of the fact that the blood supply was detached from the nipple/areola complex and initially because your nipples where covered for a period of time.
As your healing progresses and the blood flow returns, the pigmentation of your nipples should return to a shade closely resembling your previous shade. If, for some reason, this does not occur, the color can be tattooed on.
Nipple tattoos are very much like what you would imagine. A color that matches your natural color is selected and, using a needle, the doctor "colors in" the area(s) that are lighter. Please ask your plastic surgeon as to whether this is an outpatient or inpatient procedure (it's generally outpatient, done in the office) and if there is any anesthesia used.