Music Theory Basics
First thing first, everything in music is either derived from or thought of in relation to the major scale. Make sure you know how to cover the entire guitar fretboard with major scales in various keys. Also, be sure to spend time using the scale to play melodies, riffs, solos and bass lines. You want to understand the scale in a musical context, not just as patterns on the guitar neck.
Major Scale Chord Theory
Next, learn how the major scale is used to make triads and build chords. The major and minor chord number system that emerges is one of the most important concepts in all of music. Understanding guitar chord progressions and playing by numbers is critical to charting songs, recognizing keys, and knowing what scales to play. Also, the modal concept (guitar modes) stems direct from major scale patterns and chord progressions. If you learn progressions correctly, you should know what parent major scale a song stems from and what each chord is by number.
This will lay a good foundation. Learning additional music theory will make more sense. And you'll really be able to map out the fret board better too. For example, if you know how triads and chords are built using intervals such as root, third and fifth, then you'll understand how to add the other scale tones like fourths, sixths and sevenths.
To get started, listen to the Guitar Theory Podcast . If this link doesn't work just got to iTunes or Talkshoe.com and search for the terms "Guitar Music Theory Lessons."
Also, you can learn a lot about applying music theory at the Guitar Theory Blog .
These resources are all free. Go get started!
Play Until Yer Fingers Bleed!
Mr. Desi Serna (Google me!)