I guess the most important thing to understand about scales is how they are made. Starting with the major scale and getting a solid understanding of it is critical because all of the other scales come back around to the major scale. You probably already knew that though. If you know how to build scales you can make them for yourself and you will be more likely to remember new shapes that you learn. If you understand how scales are made you will progress naturally from one scale to another. Before you know it you will know more scales than you thought you could.
Learning a few scales very well in a few positions is way better than knowing a boat load of scales and not being able to do much with them. Maybe try focusing on just a position or two for a while. If you know them in side and out you have an edge over most of the guitar players that I have met.
Training your ear and working on your relative pitch is also very important too. If your ear know exactly which note it wants to go to and you know the scale shape that you are playing intimately you will be able to go right to that note.
Love to hear any other tips you've come across.
Laters,
Nate
Take a look at the Practice Routine Generator at www.BeginnerGuitarSystem.com