All we would need to do to Neryam\'s system to add in theory would be to have two stocks instead of one. You would have your skill/adeptness/ability bar and another bar for theory.
Theory goes up when you learn something. There is a high probability of you learning something when you are taught by a teacher, and a smaller probability of spontaneously being inspired on your own.
Skill goes up when you apply knowledge. There is a certain probability that knowledge is taken from your theory bar (making it go down, i.e. \'un-applied\' theory bar). This probability might be arbitrary, or it might depend on the ammount of knowledge you have stored, for instance, going up when ideas are so abundant that they simply beg to be applied. Theory might even be applied without actually using the skill (it has been shown that this happens in reality under certain conditions).
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Also, if you\'re up for some light reading...
http://forums.arcane-order.com/viewtopic.php?p=5844#5844