[Jongpil Yun]

IMO it's better just to learn notes and intervals across the fretboard.

For example, I know that in C Harmonic Minor, the b3 is on the 11th fret on both E strings, 6th fret A string, 1st fret D string, 8th fret G string, 4th fret on both B strings.

[Rayder]

^^^
well that is relatively simple. you just have to know how to count intervals from any root note. the minor 3rd in a C Harmonic minor scale is Eb. this is where i was saying before, without a good knowledge of the fretboard you are stuck. but i am learning all this slowly, and i know i will get there

[Wiz]

You have to know what notes the scale is exactly made of, in your head. So for example if you're playing a C major you know that you use all the unaltered notes. Once you know that, run around the fretboard in various patterns that you can come up with, so that you completely forget about the existence of boxes. Blues is a bit different cause most peeps find the two main fingerings / boxes to be more than enough, but usually you don't want to do that, especially in jazz. Take a scale you like, choose the key that has the fewest alterations (at first) and screw around with it for a while. You can do:

1) Diagonal runs (with a limited # of notes per string or as many as you like)
2) String skipping
3) Never using same string or adjacent strings twice in a row.
4) Other patterns you come up with.

Once you're done with one simple scale (again like C major) go with F major and G major, then D major and Bb major and so on. Switch between one and the other on the fly without stopping so you hear the difference right away. If you do this a lot, for a long time and consistently you will have the picture of the fretboard in your head, the so called frets that light up when you have a certain scale and key in mind, so that all you do is basically play on those notes that are lit. If you're like me (and probably everybody else) and you started with 3 note per string boxes for basically every scale out there, practicing this method and trying to forget about the boxes will be a total paradigm shift for you which will free you from the memorized fingerings patterns. The whole purpose is to completely forget about the fretboard, but to just feel it. Just like when you're typing on your keyboard you don't really think about where the keys you're pressing are, cause you just know they are there, same process should be applied to the guitar. It's probably one of the hardest things to learn well, but it pays off so immensely.

I think Satriani mentions something about it here in this video. It's funny how I was covering that with my jazz guitar teacher and then I saw satch explain something relatively similar on youtube that same day.
YouTube - Joe Satriani's Guitar Tips

[Durero]

^good post