Ok, here's something you can do. I call it a "TV" excercise [that's my name for really REALLY boring, repetitive stuff that you can do pretty much without thinking.]

There are a few patterns that apply to scales. Let's just start on the fifth fret of any given string.

5 6 8
5 7 8
5 7 9

Now practice those three patterns on ALL of the strings until they are comfortable. I suggest doing them one at a time, on each string so you get a hang of how the same pattern feels on different strings. Once you have those three patterns down, you know all the patterns to play at the very least the modes of the major scale... then it's just memorizing the order in which the patterns go to learn the scales.

It's important to know that patterns for scales are meant as a foundation to build off of, not a strict set of rules. Once you learn them across the neck, try figuring out for yourself how to play them up the neck on 2, 3 or 4 strings to really begin to unlock your playing.

If the scale you are practicing is pentatonic then you are dealing with two notes per string patterns. So the patterns will follow something like;

5 7
5 8

I recommend at least using two strings at a time to develope phrases...

A|-------5-7-5-----
E|-5-8----------8-5

or

D|------5-7-5-----
A|-5-7---------7-5

or

e|------5-8-5------
B|-5-8---------8-5

just play the scales.. or learn songs that go up and down on different strings, it just takes time. eventually your fingers will get used to where they're supposed to be and you can concentrate on your picking hand, or vise versa. just work one then the other.