Try this scale. I am a beginner BTW. Pinky on the root note of the major scale on the E string; index (2), ring (3), and pinky (4) fingers on the A string; index (5) and ring (6) fingers on the D string; index stretched down one fret (7) and index (octave) on the G string. The root and octave are comfortably positioned. You can go higher to the 9 and 10 or easily go below the root to the 6 or even the 5 with a two fret stretch or slide.
Ah, I just reread your original post, and you had said you already know the scales, but want to know how to use them. Well here's a beginners point of view.
1. I pick an interval from the scale such as 8, 5, 2, 6, 3, or 7.
2. I figure out what note of the scale this is for every chord.
ex. Key of A (ABC#DEF#G#A): the 2 of A chord is B; 2 of Bm chord is C#; 2 of D chord is E; 2 of E chord is F#; 2 of F# chord is G#
3. I practice playing the root, the interval, the octave, the intervals octave through a progression.
I let myself do whatever I want as long as I hit root or octave of each chord when it hits.
ex. A chord starts and I play the A on the second fret of the G string, then the B above it, then the B below it then the A and so on until the let's say E chord where I play an E then an F# above or below and E octave.
4. Once that's firmly in place, then I add in scales and arpeggios.
e. I start on the A note of the A chord go to the 2nd interval B, then ride the scale down to the B below, using scales to link things up. When I practice, I play more scales than you might if someone were singing or soloing over you; I pull back a bit when it's the real thing, but I am prepared.
I am truly a beginner. Have been playing for a year and a half. And I don't know if this approach sounds good or not, but it sounds good to my beginner ears.