With the CAGED Chord System, you'll learn your first basic open chord shapes: C, A, G, E and D. F and B are not include because in order to play them you need to create barre chords, which are important, but you'll have to learn them in order to properly learn the CAGED system. Also, the shape for the B barre chord is covered by the D shape, and the F barre chord is covered by the E shape.
By learning the CAGED system, you'll understand where to find chords across the whole fretboard, while you get introduced to the positioning of notes within the guitar neck. Make sure you learn these shapes by heart and that you can play them flawlessly; these are a pre-requisite for the next step.
http://www.jefjamdesign.com/CAGED/index.html
Once you know and understand how the CAGED system works, you'll be able to easily visualize the major arpeggios. Playing them freely will unlock the next step.
http://www.tyquinn.com/2009/arpeggios-the-caged-system-part-5/
After understanding the arpeggios, you'll soon realize that you're only missing a couple notes on each shape in order to have the full scale.
http://www.guitar-tutorial.net/diatonic.html
Finally, once you know the CAGED System, the major arpeggios and the whole diatonic scale, you can use Pitch Axis Theory to learn and use the modes of the diatonic scale.
The modes are also called "degrees" of the major scale, and they exist in order:
IONIAN (major), DORIAN, PHRYGIAN, LYDIAN, MIXOLYDIAN, AEOLIAN (natural minor), LOCRIAN
The video below explains how to take the diatonic scale, and untap the modes by shifting the position of the root note within your scale.