First off,
If this is not really a forum for beginner questions I apologize and please feel free to delete this thread. If you don't mind answering it, however, it would be much appreciated.

Okay, a little background:
I have been "playing" guitar for about 5 years now. By that I mean I've learned a few chords and a few easy songs. However, I just don't want to be that kind of guitar player anymore. I want to understand the theory. My goal is to be able to play what I feel without having to think about it, as I play to relax (which i know will take much practice!).
Having said that, I've really enjoyed watching some of Peeber's videos. I found it originally after reading that chromatic scales were good practice. I, of course, youtubed this and going through many videos I saw Peeber's. So now I'm starting the syllabus and watched the scaletone form systems part 1 and 1A. While I understand the patterns or "forms," I don't understand any of the theory behind them. What it boils down to is that I would like to learn said theory. Does anyone have a suggestion on the best way to go about doing it? Should I just sit down and read a book on it (and if so, what book?) Or should I just follow Peeber's videos and let the theory come in time? I plan on taking private lessons when I can make time (I work 50+ hours a week and have college 3 nights a week currently) but for now I think working on theory could give me a good head start.
Also, as an aside, when I first started playing, I read in many places that you should keep your thumb near the low e-string to help mute it when needed, but now I see everyone saying that you should keep your thumb behind the neck. I am trying the latter now but after playing the other way so long it seems difficult. Which way do you suggest playing?

Thanks for your time, I know it was a long read.
Brandon