I was wondering if some of you could help me out. I've been learning scales and so far have learnt the 5 different positions of the Major scale and the 5 different positions of the Minor Pentatonic scale.

I have been trying to learn the Minor scales but I'm becoming confused very quickly.

I have been reading this website: http://members.aol.com/snglstringtheory/archive/aug2.html

It shows the 5 Box positions of the minor scale. But beside each box it says "root note on 6 string" or "root note on 5th string" or "Root note on 4th string" etc. My problem/question is -- do I always start on the root not. For example if the root note is on the 4th string do i play the scale from the root note on the 4th string, or start from the 6th string and play the whole box position?

And if you do play the whole box for each position wouldn't that make it a mode since you're not starting on the root?

I'm pretty confused but really want to learn so any help is appreciated.

Minor scale "D-shape" (root note on the 4th string)

the scale starts where the one is, then two then three etc.
the notes on the lower strings are part of the scale just in a lower octave and so you cant' start on the first note
Thank you very much. So If I start on the 1 on the 4th string I can play up to the NEXT octive (past the 7 notes of the scale) but I just don't start before the 1?

Does this also apply to the Minor Penta tonic as well? Because the way I have been playing all 5 Positions of the Minor Pentatonic I have been starting on the 6th string, though I now fear I have been doing it wrong.
Scales are notes? the shapes are just common ways of transporting those notes onto the fretboard. So in reality you can start the scale on any string you wish

How much music theory do you know?

The more you know, the better, IMO. www.musictheory.net is a fantastic website for theory. The more theory you know, the easier time with music you'll have (again, IMO).