So, for example, I can roll 1d6 to attack a creature with a spell--or if I use my arcana skill along with that attack, I get a modifier, like 1d6+1? I think that works nicely. The only thing to think about is how often players will do that; if a normal roll isn't worth doing without the empowerment, players will add their skills to every roll.
Which is fine, actually, it just means that players need to be careful about how to choose their skills. If you want to make it so that players can't always add their skills, you could give them a set number of such uses per day, maybe equal to their attack stat or something.