Last year there was an article on malibu's website on gelcoat repair.
It doesn't take all that long, no worse than waxing a car I suppose. You'll need a few pieces of 0000 (4-ought) steel wool, some very high grit sandpaper (1000 to 1200), lower grit sandpaper (200 grit or so), some rubbing compound, 3M Finesse It II Finishing Material, 3M Marine Ultra Performance Paste Wax, some rags and towels, and a garden hose.
Wash the boat to clean the areas you need to fix. If the scratches are really deep, wet the coarse sandpaper and sand out the scratches. The color goes all the way down to the fiberglass, so unless you really dig deep, you won't get all the way through the gelcoat. I keep the affected area and the sandpaper really wet, either with a squirt bottle or the garden hose. If the scratch is deep, you might have to start with the coarse sandpaper, and then move to the finer stuff. With the smaller scratches, the fine is sufficient to begin with. Once the scratch is gone, the 0000 steel wool is used (also wet) to smooth out the gelcoat where you've used the sandpaper. (For some light scratches, steel wool is all you need.) Then, use the rubbing compound (following the directions on the bottle) to buff out the micro-scratches left by the steel wool. Wipe the area clean.
Next, apply the 3M Finesse It II finishing material to take care of any remaining scratches left and give it the "wet look". A machine buffer helps a lot, but it's not that hard by hand either. Then, apply the 3M Marine Paste wax per the directions on the bottle.
You can also clean up the rub rail with these materials. If yours is like mine, the rub rail takes abuse and can look awful. Take the 0000 steel wool (keep it wet) and rub the rub rail until the marks disappear. Then, go over it with the marine paste wax to make it shine. It's incredible the difference a clean, black rub rail can make.
I found the article I used: http://www.malibuboats.com/nwsart.asp?ID=3&ArtID=65
It's for gel coat repair, but I ignored that part and adapted the scratch removal. Good luck!