Now, I'm far from a professional, and not terribly experienced in music theory so dont take my word as gospel here, but when you are looking at the shapes of the various scales, the root notes are going to fall onto those lowest strings. That doesnt mean you cant start on say the d or g string, and make a note on those strings your "root" while playing through a scale, but for the sake of seeing the whole shape on the neck, I believe that you would say the root is on that e and a string, just because from there you can see the entire shape of the scale in question across the neck.
So...to think about it this way, play through your scales, and wherever you start them just look at the shape you are using and follow it backwards to see what scale that might be.
Again, I may not be correct on this so if anyone else can correct me (GT instructor staff :P) please do....I would appreciate being corrected myself so i would know...