I like to pick it up as I go. If you're working on scales, that will happen automatically. Remember to think of the octaves too because they're the same note, this cuts down the learning curve, then you can connect the dots as you move ahead.

This lesson on 'visualizing fretboard scale patterns' by Christopher Schlegel is helpful:

http://www.guitartricks.com/lesson.php?input=11094&s_id=419