One thing I learned a long time ago was my fretboard, in terms of all the scales in all the positions... You have to learn it - there are no two ways about it. I shift between positions so easily now that I really don't have to think about them much... I would suggest starting your scale education with the major and minor scales, and after that, diminished, augmented and whole-tone. Then depending on what kind of music you want to play, the modes should be learned. My theory about this kind of thing is that you should learn it all. Once you've learned it you can play whatever you want to play, and I think that your playing will be more advanced, and you'll have a better understanding of the instrument.

Denyer, Ralph (2002). The Guitar Handbook. p. 102. ISBN 0-679-74275-1.