Michael (aka Merlin) post this via email and it somehow came to me so I’m “Reposting” it here for him..
If I had a gel coat scratch deep enough to require filling, I would start by filling it with a “surfacing putty”. Auto body fillers come in (at least) three densities. The thickest and most commonly found in hardware stores, auto parts stores etc. (Bondo, Pink Lead, Kitty Hair etc.) are way too thick for small scratches. Go to an auto paint supplier. Next level is for surfacing, You can purchase it in small cans or tubes with a tube of catalyst. If you mask off the exact edges of the scratch and carefully apply it, this product should be thin enough to fill a deep wide scratch (1/8″x1/8″deep?). Just use that tape so you don’t get the stuff on the surrounding gel coat. Hand sand it smooth before you remove the tape. That’s a little tricky because the tape itself has a certain thickness; just bear down on it a little. When the tape is about gone at the edges of the fill, you’re there. If you were careful you should have it level.
Clean off the adhesive left behind by the tape with a household cleaner. Apply the touch up paint you had color matched at the auto paint supplier with an artist’s brush and you should have a repair which although not invisible will be unnoticeable from 10 ft. away. Step one is to drive the car to an auto paint supplier and throw yourself at their mercy; they should have everything you need including the little brushes. Ask if you can take the color sample book out in the sun and look at the colors next to your car in natural light. If the scratch is small enough, there’s a product which comes in a tube and doesn’t even use a catalyst. I’m never shy about asking for advice and my local paint supplier seems happy to provide it; I just don’t go in when they are busy. All the plastic auto body fillers work fine on fiberglass; which is essentially what they are anyway. Or, take the car apart, sand the fender’s gel coat with 100 grit, prime, paint etc. Not worth it for a scratch. Hope this helps. You’ll end up spending about $30-$40 bucks I bet. I backed my truck into my Shopsmith once and it cost me $400.00.