Watch the Making Music with Scales online guitar lesson by Larry Carlton from 335 Improv
Probably the most dangerous thing about working with scales, especially for guitarists, is that a player can end up running scales instead of creating music.
Think of scales as groups of notes to choose from as you solo. Don't think of them in linear order, either, because you may develop a tendency to play them that way: up and down, in straight lines.
Instead, listen closely to how each degree of the scale works against the chord - and then think about how you tie those notes into the next chord. Where are the common tones? Which notes sound great to sit on and which should you avoid? Which bends work between the two chords? How will you incorporate an interesting note from the scale into your melodic treatment?