My understanding on how these things works is thus:
With PCMs, that only determines how a player might do when he is created. This is for potential and current ratings. However, over the course of a sim both those things change. So, while you might have put the PCMs really low, through the natural course of development the player might actually get a lot higher potential and current ratings then you intend, and you will then have players who are doing extremely well in a league that you don't want players like that.
Which is where the League Totals come into play. If you don't want that many hits, homeruns, ect. it's MUCH better to change these. They will artificially make the league a lot worse/better then it is. You still might occasionally have that anomalous player, but they should not be too far outside the norm.
Now, that's how I understand things as I have read them. You can check the manual it I believe it actually goes into a little more detail on these things because I read a discussion about it when Steve was trying to put together that part of the manual.
