A players best position has nothing to do with training. It is only a suggestion to let you know on which position a player will make the best use of his skills. So, only minutes played at trained positions count.
The training effect on your PF and C will be the same if they both have played over 48 minutes (or the same ammount of minutes under 48, for that matter), but there are a lot of "if's": age, height, in the long run potential (and I am sure I am forgetting a couple of things..), all influence training efficienty slightly, even if both players play over 48 minutes.
I hope this helps!
Please use the help forum
(5542.1) the next time you have questions like these.