That's where my struggle is...being able to take what I know and learn and apply it when I am playing instead of relying on my ears so much.
The thing that most people will tell you is that you learn the theory and then you "forget it" and just play. What you know will flow out naturally.
Again, like I learned in my class, dissecting songs and understanding the theory inherent in them is a good way to learn about theory in regards to chord progressions, scales, melody, harmony, etc...
Any honest musician will admit that learning theory isn't so much about rules, it's about freedom.
