Like many guitar players i'm awful at practicing scales as it just bores the hell out of me. So, what do you experienced players recommend to not only practice scales but also how to ACTUALLY learn them? What i mean is not just being able to play the box shapes but how incorporate them into your playing in different positions.
Well,what i found worked best for me many moons ago was to improvise to backing tracks.Make music,This not only helps you remember your scales but it gets you learning to use those scales in interesting ways and develope your own style.Start in one position and then get jamming until it is embedded in your muscle memory then move up to the next.When you have all the positions down practice using the whole scale up and the neck to make music.
If I was learning a new scale I'd learn it by using it to improvise over a backing track, and playing music with it. The whole reason you use scale X vs. scale Y is because the notes sound different over a certain chord or progression, so working on one with no chord or progression in the background seems kind of pointless to me.

(Oops, looks like Eyeballpaul beat me to that one)

If you were learning to play (for example) the pentatonic minor scale over a I IV V progression, I'd print out some fretboard diagrams, draw out the notes of the scale on 3 diagrams, and then on the first diagram use magic markers to highlight the notes in the scale that correspond to the notes in the I chord, then on the second diagram I'd highlight the notes of the scale that correspond to the notes in the IV chord, and the third diagram for the V chord. Then when you play over that progression, try to end your phrases on notes that correspond to whatever chord you're currently playing over.

It wont' take long before you start developing an ear for that and hearing how the notes of the scale interact with the changing notes of the chords you're playing over, and then you can start creating tension and resolution and really sound like you know what you're doing.

Also pay attention to where the root notes are, as you'll find the same arrangement of notes located around each root note (with the exception of the ones on the two high strings which, because of the tuning differences, will be offset by one fret). If you know where the root, 3rd, 4th, 5th and 7th are located in all their different positions all over the fretboard, then you can continue a musical phrase uninterrupted while moving around all over the place.
Last edited by gtc83 at Jun 16, 2014,
mixing chords and arpeggios with scale practice really helped me connect shapes and sounds. it's kinda fun because you're building your own understanding of the fretboard, and you might run into cool practice patterns while doing it (e.g. up an arpeggio, down a scale). but you need to already be comfortable with some basic shapes before you'll be able to feel like you're accomplishing anything this way.
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I'm learning the pentatonic scales in the open position. I pretty much have them memorized and I ran into the same problem you are having. Based on my talks with my teacher I found the best way is to run up and down the scale a few times and then just try puttin your own rythmn to the notes. Basically at that point ur making a solo. Now I just need to move to another scale to move along in a progression. Look at the songs my girl and wish you were here. The whole rythmn to the song is just a straight up pentatonic scale with a rythmn to it. My girl is open position c maj pentatonic and wish you were here is open position g maj pentatonic. Its amazing that such a great song was probably written by doing what we are doing, running up and down the scale trying to put a rythmn to it.
Practicing or using?

The best way to practice scales is to run them up and down the neck non-stop, starting at the lowest position possible (even if you're not starting on the root of the scale). If you're playing, say, A major, start on the open Low E string, play up to the G# on high E string, move up to the next position, and play back down to the low E string, move up to the next position, etc.

But that's more of a technique and fretboard knowledge thing. I run scales about 15min a day as a warm up, just because it's an easy way to cover the whole fretboard and work on both left and right hand technique.

For using scales, you need a very different approach, though it's still required that you first know them thoroughly.

You're pretty much never going to just run a scale up and down in real music. When you use scales in music, what you're really doing is using specific notes from the scale to play within the harmony defined by song's chords. This usually means playing chord tones, often all from the same scale.

Say you have chords C, Dm, and G. Key is C major, and those notes are C D E F G A B.

Take those chords apart:
C = C E G
Dm = D F A
G = G B D

and then see how they each fit into the scale

C = C D E F G A B
Dm = C D E F G A B
G = C D E F G A B

Whenever your chord changes, you change which notes from the scale to emphasize. Sometimes you'll just play a plain old arpeggio of the chord, and sometimes you'll throw in other notes from the scale for melodic interest.

Exactly how you use the scale is up to you, but the basic idea is to use it to support and emphasize the harmony.
Put a track on, even if you just go up and down in 1/4 notes, it's less boring with music