Welll... that's a complicated question. It really relates to how the fretboard is laid out, and I've found primarily that what it takes is a shift in how you think about the fretboard, and a lot of practice. And I'll state for the record that this isn't something I'm particularly skilled at, but it has been a recent focus of my practice sessions, so I can only share with you the strategy I've taken to address that weakness in my playing.
I have taken the view that there are only five scale patterns for modal scales, period. For the purposes of this exercise, I have abandoned any notion of key, and focus purely on those five patterns, as all modes can be played using them. Since I'm a CAGED method kind of guy, I like to think of those patterns in terms of the chord shape they relate to. The C pattern, the A pattern, the G pattern, etc...
This makes it much easier to tie the scales together, as that is how they "flow" down the neck. For example, play an open C, then play C at the 3rd fret (the "A" shape). Then go back and play the C scale in the open position using the C pattern, and then play it at the third fret using the A scale pattern. You've just extended your "box" by one position. Move down the neck and play C at the 5th fret using the G shape. Play the C scale there using the G scale pattern.
When you can play those 5 patterns well enough that you can move down the neck fluidly, then then next step is realizing where on the scale you wish to start. The best way to do that is to know where the root is for any of those 5 shapes. I know when I'm in C that the root is on my index finger and pinky, for example. For E and G shapes, it's the index finger or whatever finger is on the Fat string (and skinny for G). That kind of thing helps you locate chords quickly. You may have heard me say that you are never more than three frets away from any major chord. This is why.
Anyway!
Want to play in A minor at the open position? That's still the C scale pattern. You're just starting your scale on the A and playing through to the A. you can pretty much play any of the modes this way.
Times like this I really wish I could link images into the forum, as it's the best way to demonstrate it.
Anyway,
Here is the C scale pattern. It's shown in the open position, but it's completely portable all over the neck. It's my personal favorite as it is a natural fit for your hand on the neck of the guitar, too. You may know it as "pattern 1."
http://chrisjuergensen.com.hosting.doma … major1.gif
Now here is A pattern, or pattern 2.
http://chrisjuergensen.com.hosting.doma … major2.gif
Imagine this one sitting two frets down from the C pattern above. Then get on your guitar and play these patterns in that manner. C in the open, and A on the second fret. You'll see how they tie together.
Now move that entire shenanigan down two frets from the open position. Same patterns, though. You just went from playing C in two position, to playing D in two positions.
So that's a lot. I hope it reads clearer than it writes. 
<------ This is there because my daughter likes it.
