O.k.,...here's how I teach it. I find it better to relate the notes to each other going from low string to high string instead of top to bottom from each string, since this is how most of us play...unless your Mr. Super Legato like Satrianni.

The neck of the guitar can be divided into 3 positions: 1st, 5th, and 9th...everything else is just an overlap of these positions, ex; 3rd pos. would just be a combination of 1st and 5th.

A position is defined by what fret your 1st finger is on.

Pos.1, playing the natural notes from 6th string to 1st will outline an E Phrygian scale;
(6)E F G (5)A B C (4)D E F (3) G A (2)B C D (1)E F G

Pos.5 will outline an A minor (Aeolian)scale
(6)A B C (5)D E F (4)G A (3)B C D (2) E F G (1) A B C
*you will have to reach out of pos. for the B on the 3rd str., but if you know the pattern for Aeolian you will already realize this. At this point you should realize that the pattern of the notes just move down 1 string

Pos.9 will outline a D Dorian scale
6)D E F (5)G A (4)B C D (3) E F G (2)A B C (1) D E F

The next pos., position 12 will be a repeat of position 1.