Watch the Music Theory online guitar lesson by Bruce Arnold from Jazz Guitar for Beginners
Music Theory is usually the weak point for most musicians and is doubly true of guitarists due to the majority of "self taught" players.
I would highly recommend you work through the book "Music Theory Workbook for Guitar" Volumes One and Two. These are the only books I know of that directly relate learning music theory to the guitar fretboard.
Mastering the information found in these books will help you not only learn the notes on the guitar but also to understand how chords, scales and arpeggios are played on the guitar and also to understand fundamental concepts like "diatonic chords of a scale" and "tensions" which are essential components in playing jazz.