Here's what I mean -
G Aeolian (CAGED)
E - 3 - 5 6 -
B - 3 4 - 6 -
G 2 3 - 5 - -
D - 3 - 5 - -
A - 3 - 5 6 -
E - 3 - 5 6 -
G Aeolian (Three note)
E - - - 5 6 - 8
B - - 4 - 6 - 8
G - 3 - 5 - 7 -
D - 3 - 5 - 7 -
A - 3 - 5 6 - -
E - 3 - 5 6 - -
So, as you can see, it's the same exact scale, just a different way of visualizing it. Some people prefer one over the other, but I've found that each has it's uses. The Three-Note is great for shredding, because you don't have to change your rhythm (it's always 3 notes per string). CAGED is perfect for chords and arpeggios.
Does that help?