To answer your question. It's best to know all the positions of each scale on the fretboard. This is important when you want to move from one scale to another on the fretboard. If you playing a E major scale on the 14 fret position on the D string and you want to go to A major. Well if you only know the scale from the open A string position, you're going to be terribiably lost. You should know the scale from the 12 fret position on the A string as well. End of problem. Knowing the pattern is good, but being comfortable with that pattern anywhere on the fretboard is more useful. Here's some ways I use to master those scales on the fretbaord.

I generally say their are 3 ways to learn scales on the guitar. The first is the most common, which is the 3-note per string scale. Take A major:

e:--------------------------2-4-5--
b:--------------------2-3-5--------
g:--------------1-2-4--------------
d:--------0-2-4--------------------
a:--0-2-4--------------------------
e:---------------------------------

Also play these from different positions on the neck. Example: Start with the 5th fret on the low E, the 12th fret on the A string. etc. etc. You don't need to start from every A note on the guitar, just at least a low octave (open A string for A) and a high octave (12th fret on the A string for A), and the same note on a different string (Open A string and 5th fret on the low E string) if that's true.

The second is playing a scale on one string only, but play that scale on each on the strings on the guitar. I'll use C# major as an example.

e:-----------------------|---------------------
b:-----------------------|--2-4-6-7-9-11-13-14-
g:-----------------------|---------------------
d:-----------------------|---------------------
a:--4-6-8-9-11-13-15-16--|---------------------
e:-----------------------|---------------------

Also play it on the D string, E string, and G string. Remember lower root to highest root, so if your play A major on an A string, you start from the open A and go up to the 24th fret.

The last is by playing from the lowest root note to the highest root note on the fret board (12 fret range, it's too hard to do in a 24 fret range, so you just split it.). Here's E major: (/ - slide, very important cause it gets you familiar with going from one position to the next.)

e:-----------------------------------------9-11-12-
b:-------------------------------7-9-10/12---------
g:-------------------------6-8-9-------------------
d:-----------------4-5-7/9-------------------------
a:---------2-4-6/7---------------------------------
e:-0-2-4-5-----------------------------------------

Now you play it an octave higher like this.

e:----------------------------------------------------------21-23-24-
b:----------------------------------------------19-21-22/24----------
g:-------------------------------------18-20-21----------------------
d:-------------------------16-17-19/21-------------------------------
a:-------------14-16-18/19-------------------------------------------
e:-12-14-16/17-------------------------------------------------------

I know not every scale will work out this perfect, just go from the lowest to the highest root possible. If you learn the modes as well it will fill in the gaps, and plus practicing the other methods will also help too.

Notes: Remember to play them ascending as well as descending. Get yourself a metronome to keep track of your progress with each scale. And another good tip is to spend at least a couple of sessions singing the scale when you first start practicing it.