I think playing chords with your thumb on the low E is really a helpful technique in blues and jazz, it helps you to reach so many different chords that would be really awkward to play otherwise and it frees up your other fingers to add fills to the chords ala Hendrix.
I rarely play a root 6 chord shape without using my thumb, its become such a huge part of my playing that I could never stop doing. That said I know how to change my grip when a chord like that is called for and then maybe even have my thumb right down the neck like classical technique if I need to do a fast run that involves stretches.
When you are learning I think it is better to play with your thumb behind the neck so you can develop proper technique and it makes changing regular chords easier than if you have your palm wrapped tightly around the neck.
Then once you have that be able to change your hand position according to the chord or line you want to play whether that be with your thumb on the low E or whatever.
-Jess
Check out my band Beth and The Black Cat Bones
http://www.myspace.com/bethandtheblackcatbonesAlso my own page for my guitar playing
http://www.myspace.com/jesszub