PokerTracker

If I make new rules in the NoteTracker, will it also apply for the hands I have already played, or just the hands I play after.

Just the hands you've played after - if you want to go back and have it apply to everything, you need to purge all NoteTracker notes and then let NT start rebuilding your notes from scratch (which it will do in the background while you play so it should be fairly painless). You can do this on the Tools -> NoteTracker -> Status page.