I am teaching myself guitar from the internet and am suffering from analysis paralysis. Different websites show different positions for scales. And then some positions start somewhere other than the root note.. so on what note do I start or stop? And then I learn about 3 note per string major scales and then I learn about modes. It's all very overwhelming. I understand the major scale formula and the theory behind it. All I want is a system for learning the scales that someone could explain to me.
As guitars can play exactly the same one note in many different places - strings and frets, there can't be definitive scale shapes.Perhaps 'definitive' isn't exactly the right word! There are scales that many people use, in the same positions as each other, but apart from that, yes, it's confusing. Have a look at the RGT grade books, which show very acceptable scale patterns, in many positions. For now,at least, scales when being learned should go from low root to high 'root' and back.It makes them sound cohesive, whether one octave or two. I suppose that's what makes them scales!
Work on scales that can be encompassed without moving the whole hand up or down, as in using fret 4-7 for A major, one finger per fret. The similar natural minor pattern needs one note on a fret lower, but it's nearly there, to be fair.
Work on major, natural minor, pent. maj. and min., and blues patterns, all of which can be moved up and down for different keys. Modes could come later, when you have that lot under your fingertips!
I recommend always starting on the root, regardless if it's on the 6th string. For example, for C major in 1st position, I would start on the 3rd fret of the 'A' string. This will help to internalize the sound of what scale you're playing since you start and end with the "home" note.
As to the systems, you really have to use what works for you (i.e. what feels natural or easiest to play and experiment with). I was first taught the rigid "3 notes per string" positions. Later, I had a teacher who preferred the system (link below) where you minimize sliding fingers up or down the fret, which means sometimes you play only 2 notes before moving to the next string. I have adopted some scales from both systems. The more you can do the better. But it may be best to start simple, and I do recommend the 5 position system here:
Finally (and this is way underrated): spend time learning the fretboard. Regardless of how well you know the notes, you can always get sharper and quicker. Play scales linearly (one string at a time) while thinking of the notes. Try playing every "G" note on the guitar. One time, I even made online flashcards to drill me on visualizing each note. Being intimate with the note names will pay dividends to your scale playing and playing in general.