It really depends on how thick the gouges are. If they are real bad, sand it out as best as possible but then use bondo or a bumper filler to fill in the bad stuff and keep the fairings structural integrity. Then sand and shape it.
Be sure to remove any paint chips or thick built up areas of paint. You want to get as close to the original fairing material as possible. If it is only one coat of paint on there that is sticking well and not peeling chipping, then just scuff it/sand it really good.
For medium scratches start with a medium/light grain and wet sand it out gradually going to a very fine grain to finish it out. When doing all this just keep in mind to blend everything together, focus on the area not just the gouge itself , if that makes sense.
For light scratches use a fine grain and wet sand it out.
Once you are happy with the lines etc. do a very fine grain wet sand or use a fine scuff pad over everything with some thing like this.
This ensures a nice clean surface which will prevent things like fish eyes etc. in your paint and will also make sure the primer/paint sticks and lasts long.
scuff the fairing up and use a gel/paste like the one above to clean/degrease/prep for primer. Wash with water, dry off, and lay down your primer. Scuff the primer, wash and dry and then lay down paint. Once dried lay down a clear coat to make it last.