Newbie Waxing/Polishing Question

If you are applying it by hand than don't worry about going through your clearcoat. If it needs to be polished then go ahead and do it. Claying doesn't actually remove any paint so I usually do that before every wax. The Meguiars Deep Crystal System is pretty good but, if you can find it try Meguiars Body Scrub Paint Cleaner in place of Step 1. If you have swirls or scratches it will be a bit more effective. The Paint Cleaner in the Meguiars Deep Crystal 3 step system you mentioned is primarily a chemical cleaner which is most effective with oxidation. The only real reason to worry about going through the clear is if it is already pretty thin for example it has been machine polished with a rotary buffer more than once or you have severe oxidation.

I sometimes think people underestimate the durability of a clear coat. I don't know if anyone's noticed it or not but they are pretty hard to go through in terms of polishing and buffing. Perhaps with a rotary buffer at high speeds with a real aggressive cleaner, but not with orbital buffers and standard cleaners.

BTW, not to hijack the thread or anything I've noticed after using Meguiars number 2 with a foam bonnet on my orbital buffer, I can see all the imperfections in my paint. It looks like my paint has slight "pits" developing in it. I think this has to do with the fact my car is black and everything shows. I've also noticed something else. If I look at the paint "here and there" I'll see a little "dot". Its the same color as the paint and very hard to notice. If I lightly "pick it" with my finger tip, it falls off and the everything looks normal. Just what the crap is this ?