You're missing the point I'm trying to make, Axl. The harmony dictates your tonal center. Whatever chord the progression seems to revolve around, or what it seems to best resolve on, that's the tonal center (ex- C, Am, F, G. The tonal center is C. Try just stopping the song on any other chord. It just doesn't sound right). Well, now that you have your tonal center, pick a mode with that tonal center as the root note. Since our tonal center is C, we can use C Ionian, C Dorian, C Phyrgian, C Lydian, C Mixolydian, C Aeolian, or C Locrian. And these modes do cover the entire fretboard. The mode of C Ionian on the fretboard is EVERY C, D, E, F, G, A, and B over the ENTIRE fretboard. C Aeolian is every C, D, Eb, F, G, Ab, and Bb over the whoel fretboard.


Those little shapes are used, because it's easier to visualize a small box than an entire fretboard pattern when improvising. If my hand is somewhere around the 8th fret, I know I have a C at hand on the 6th string, so I can use one of my little mode boxes. If I was around the 3rd fret, I use that box starting on 5th string. If I was able to just visualize the entire C Ionian scale over the fretboard, then there'd be no problem, but I'm not there yet :)