I learned each mode first, for example when I wanted to play the note G in a certain mode, I could switch the desired box to the desired note as Jarsew describes

other then that I did what Neal Walter is using for chords, you've got the three open chords that, combined with barre chords, can make most chords on your fretboard, inversions excluded of course..

learning all the notes was a bit too much for me, but might be a very good way to combine music theory with practical implication, so you're beginning to see how chords and scales are build