Here's the scoop...
Sometimes, for various reasons (UV exposure, chemical composition of the gelcoat, how the gel cured in the mold, etc) the gelcoat will become porous. If you look at it under magnification you can see it. By using bleach, oxalic acid, muriatic acid or whatever else you are simply removing the stain from the pores. The pores in the gel will accept any kind of contamination and will either mold or rust or cause some other chemical reaction that will discolor your boat.
Esentially, your goal when buffing is to remove this top porous layer of gel, if it's really porous you may have to wetsand, but most likely not. The Perfectit III says that it will take out 1200G scratches BTW.
So... you have to do what ever it takes to get down to a solid non-porous layer of gelcoat. I hardly ever have to wetsand, but it takes perfectit III, a serious buffer, some time, and some good solid pressure. You have to watch that you don't heat the gel surface up too much when buffing; it will get hot if you're doing it right. Check this video if you haven't, I am pushing so hard that the pad is bending and the hull is moving:
http://www.youtube.com/watch?v=74sEyot5A_oI'm sure your boat is better than the one in the video. It sat in a field in direct sun for 20 years!
Keep the pad clean, don't let it load up. Take your time, get it down to solid gel!
Once you get a serious shine (ie. You're down to solid gel) then, and only then are you ready to seal. By putting wax on afterward, you are sealing up the new surface and hopefully slowing the oxidation process so next time it's much easier to clean. And you're making it so that all those chemicals, minerals etc that we sail around in don't get a foothold to cause stains. It's work, but it will save you time in the long run, and your boat will look nice.
Oh, and if your boat is painted and not gelcoat, don't even touch it with the perfectit III. Just don't.
Hopefully that clears things up...like that pun?