Now, a lot of beginning guitarists will just learn the shapes, and get fairly good at playing in one shape at a time, but they have trouble fluidly going from one shape to the next. They'll have a hard time being able to play rapidly all over the neck or jump from high up on the neck around the 17th fret down to like the 5th fret.
The way to really understand the fretboard is the see how the shapes connect together. I think it is very important to see how all these boxes connect together, what notes they share in common and the patterns everything follows.
I'll start with the first two boxes of the Major scale to demonstrate.
Code:
_______________
/ 1st Position \
|-7-|-R-|---|-2-|---|-3-|-4-|
|---|-5-|---|-6-|---|-7-|-R-|
|-2-|---|-3-|-4-|---|-5-|---|
|-6-|---|-7-|-R-|-3-|-4-|---|
|-3-|-4-|---|-5-|---|-6-|---|
|-7-|-R-|---|-2-|---|-3-|-4-|
\___________________/
2nd Position
As you can see, the the two positions fit together perfectly. You just have to look at what all notes they share in common and remember how they fit together. The 1st box pattern matches up with the 2nd. The 2nd fits into the third, etc. until the the 5th box fits into the 1st.
I've made a chart for both the Major and Minor scales to show how all the patterns fit together.
Here's the Major boxes
Code:
/ 1st Position \ / 3rd Position\ / 5th Position \
|-7-|-R-|---|-2-|---|-3-|-4-|---|-5-|---|-6-|---|-7-|-R-|---|-2-|
|---|-5-|---|-6-|---|-7-|-R-|---|-2-|---|-3-|-4-|---|-5-|---|-6-|
|-2-|---|-3-|-4-|---|-5-|---|-6-|---|-7-|-R-|---|-2-|---|-3-|-4-|
|-6-|---|-7-|-R-|---|-2-|---|-3-|-4-|---|-5-|---|-6-|---|-7-|-R-|
|-3-|-4-|---|-5-|---|-6-|---|-7-|-R-|---|-2-|---|-3-|-4-|---|-5-|
|-7-|-R-|---|-2-|---|-3-|-4-|---|-5-|---|-6-|---|-7-|-R-|---|-2-|
\__________________/ \_________________/ \_____________/
2nd Position 4th Position 1st Position
And the Minor:
Code:
_________________ _________________ _________________
/ 1st Position \ / 3rd Position \ / 5th Position \
|---|-1-|---|-2-|-3-|---|-4-|---|-5-|-6-|---|-7-|---|-R-|---|-2-|-3-|
|---|-5-|-6-|---|-7-|---|-R-|---|-2-|-3-|---|-4-|---|-5-|-6-|---|-7-|
|-2-|-3-|---|-4-|---|-5-|-6-|---|-7-|---|-R-|---|-2-|-3-|---|-4-|---|
|---|-7-|---|-R-|---|-2-|-3-|---|-4-|---|-5-|-6-|---|-7-|---|-R-|---|
|---|-4-|---|-5-|-6-|---|-7-|---|-R-|---|-2-|-3-|---|-4-|---|-5-|-6-|
|---|-R-|---|-2-|-3-|---|-4-|---|-5-|-6-|---|-7-|---|-R-|---|-2-|-3-|
\_____________/ \_____________/ \_________________/
2nd Position 4th Position 1st Position
It really takes a lot of finding ways for you to remember for yourself, so find as many patterns as you can to help you remember how it all fits.