What about marine putty? I've used it on those plastic bass tender boats. it sticks extremely well and can be sanded. I got it at wally world. It's the type where you cut off what need and then roll it in your hand to mix the two components.

Now I don't know how many scratches you're talking about and how long they are but this should work for a few deep gouges. It works very well on holes. I've used it to fill in holes on my transom from old transducers.

If the damage is primarily down the center of the boat you may also want to consider glueing on a keel saver. That will cover and protect any weak spots.