Always start with a clean surface. Wash thoroughly with soap and water, and rinse clean. For an effective but mild, all-purpose soap, try TotalBoat Boat Soap.
If there are stains in the fiberglass that the soap and water didn't clean, it's best to try to remove the stains first in order to limit the amount of gelcoat removed while polishing the stained area.
Be sure to use a stain remover made specifically for fiberglass/gelcoat, such as TotalBoat White Knight fiberglass stain remover.