Buffing out scratches can be a difficult process. I'm not sure of the factory instructions. The first step is to determine if the scratches are as deep as the thickness of the Gel coat. If the scratch is deep it may be hard to make the scratch disappear. My procedure for scratch removal on a colored hull is determine how deep the scratch is. To deep, I compound, polish, wax. A heavy compound with a wool pad. Compound a large area around the scratches to help blend. This should polish the scratch making it less noticeable. The issue with using a heavy compound is, it leaves swill marks that look like fine scratches in the finish. To remove them use a polishing compound. If it is a small area I use a 5" foam pad white color. This will remove the swirl marks and fine scratches. The final step is a good wax/protectant. Apply the wax, let it haze over, then use a polishing pad or a foam pad black in color. If the area looks better but not good enough repeat. After second application that is as good as it is going to get.
If you feel the scratches are not to deep and the scratch does not penetrate close to the fiberglass then uses a1000 grit wet sand paper. Sand the scratches out. Don't sand only on the scratches move out several inches and sand a wider area to blend the scratches with the hull. This helps prevent from sanding through the gelcoat and removes the scatches and evens the surface. Once you see that the scotches have blended into the surface go over the area lightly with 1500 grit paper to reduce the sanding scratches. Using a heavy grit compound buff the area with a wool pad. Move outside the area that you sanded to blend the surface. Polish until you see a good shine. Use a polishing compound to remove fine scratches and swirl marks. Using a soft rag hand polish and look at the results. You may have to repeat the compounding and polishing again. Once you are satisfied with the outcome. Apply your finish wax protectant.
Touching up scratches in gel coat does not work! You will always see we=here you touched up and it will look worse that the scratches. If you want to apply a new finish to cover up the scratches practice on something else first. There is an art to Gelcoat work. It needs to be mixed to color match, then applied by spraying using the correct amount of hardener and thinner. Then wet sanded and buffed. For most folks this is a job for a professional.
Good Luck