Well, I tend to get some rub-throughs no matter what I do. But on the latest one I did put on extra much clear coats, almost a full TS-13 can...some 5-6 wet layers. This gives more paint to work with when you polish it out.
My method is to start with the finest polishing cloth that will do the job, no reason to take the most coarse one if the finish is without or has little specks and orange peel.
Then I work my way down to, say 4000 or 6000 grit before polishing with Tamiya compounds and finish with Bare metal's plastic polish.
Use some kind of sponge to support the cloth when sanding and avoid going to hard near sharp edges, some says you could put on some new paint if you rub through but I have never had any succes with that.
The key words are slowly and careful and you should be fine, the worst thing that can happend is that you have to do it over again.
One more thing, don't try to repaint over a polished bodywork....you'll most likely end up with fish-eyes in the new paint job. The compound seems to leave some ressidue that spoils any attempt to paint over it.
Hope I made any sense with this!?
Good luck and show us the progress.
Niclas