I teach my students the modes in major and minor and then once they are used to those fingerings I teach them how to link positions together and expand the entire fretboard to use the whole scale. Focusing on certain positions will give you a certain effect in relation of melody to harmony but most students starting out don't really want to focus on it that much. They just want to play. Also notes repeat over the fretboard so I try to make it stupid simple for my students to put to use the scale they are working on in a musical situation. So really I try to look at the fretboard as a whole and not chunks. It's more about being free with it than using certain modes over certain scales.
A sample from my tutorial on Modes: http://www.youtube.com/watch?v=X0Xj-xGpLhw
Joe Pinnavaia
www.digital-nations/artists/testtuberhino
www.guitarlessonsbuffalony.com
