Al - How did you go about learning? I would love to learn the theory side. I took three years of lessons in college and I have done some self taught stuff but I am very sketchy on my theory. I have never found a good way to remember it. I bought the book "Fretboard Logic" and I have been reading it and practicing some of the CAGED exercises, but the back-to-square-one aspect of going through that program is kind of frustrating. The way it is set up, you can't really skip around.
Also, do people use this in application? I mean, obviously when writing or composing a piece of music they do. However, I take a lot of my solos and improv them. I have certain landmark areas that i play the same each time, but between those I usually just play around using a pentatonic base with half and full steps added as I feel (or mistakenly stumble into). I am comfortable moving up and down the neck but I don't think of the actual "form" as it moves up and down the neck. I've just learned through practice and trial and error where the relationships are in relation to Positions 1 and 2 (what CAGED method calls "G form Pentatonic" and "E form Pentatonic").