I think it depends on how deep the scuffs are. I'm right now doing some similar repairs, so I have a few thoughts.
If the scuffs are not very deep I would try to determine if the area could be sanded flat without having to go very deep. I'd use a small wooden sanding block, even as small as 3/4 inch by 3 inches and use sandpaper going from 120 through 150, 180, and 220 grit. If you then finish with 320 or even 600 it should be ready for the rubbing compound.
If the scuffs are too deep I would be inclined to deepen them with a Dremel and a circular burr then fill with epoxy (or gelcoat). If the surfaces are vertical I'd pick up a can of West System 404 sillicate powder and mix it in until the epoxy is thick enough to stay put. Then do the block sanding sequence until it is level and smooth. Then 2 or 3 coats of Interlux Brightside over some proper primer, eventually buffing it out.
You could try some Gelcoat instead of the epoxy. I haven't yet, but it seems you have to get the right type so that it will harden properly. Some types need to be covered with wax paper to cure. Good luck!
The real trick to getting a good job is using a flat block to wrap the the sanding paper around.
These are just some suggestions, since it is hard to know what to say without looking at it.