I agree with the above poster. Learn the intervals, but at the same time, it is really important to begin memorizing the fretboard and all of the notes on it. Start with the natural notes, that is the easiest. I like to do one string scales or improvise using only one string, for example E phryggian, while being fully aware of every note. E phrygian is all of the natural notes. Play D dorian, A minor, and G Mixolydian, too.

Then when you are playing the scales while memorizing the intervals, you will see, hey that is a sixth above the root (let's say C), so it must be A. Learning the intervals for each scale is also very important. Once you know the 3 and 4 string patterns for every interval in a scale you will be really close to getting it all, because the intervals start over again.

The 3 string pattern ends on the close octave and the 4 string one ends on the far octave. The intervals from string to string never change, but each note's function within the given mode will change depending on the context. for example the 6th of a Major scale will become the root of a minor scale within a minor chord progression, but the interval between C and A will always be a major sixth or a minor 3, depending on which inversion you use. Both of these skills are part of an ongoing process to really have control of what you are playing on guitar. music is great :)