Originally Posted by: Itsmesillyright now I am working on learning and knowing the major scales and the order of sharps and flats....[/quote]
It is better start by simply understanding ONE major scale, the C major scale. Then, realize that every major scale has the same formula and therefore pattern on the guitar.

The different sharps and flats are merely a result of applying the scale formula to each musical alphabet note at a time. Put the 1 of a scale on a G note, apply the scale formula and you will get the same pattern as a C major scale, but with the scale degrees (the circled numbers of my lesson diagrams) on different musical letters.

1 - 2 - 3 - 4 - 5 - 6 - 7 - 1
C - D - E - F - G - A - B - C
G - A - B - C - D - E - F# - G

And so on. But it's the same pattern on the fretboard however with the 1 (the scale root note) moved over from a C to a G.

The reason every scale has it's own unique system of sharps and flats is a result, a consequence of the more important and fundamental concept: the scale formula.

So before you torture yourself trying to memorize the notes and sharps and flats of 12 "different" major scales and 12 "different" minor scales ... grasp this concept first: every major scale has the same formula and therefore pattern on the guitar. Learn the formula and how to apply it anywhere on the guitar fretboard. Play it all the time, draw it when you are away from your guitar.

Originally Posted by: Itsmesilly
my question is this.....if I know where a note is on the guitar....and I know what notes are in a particular scale...then can I just find it on the neck and move to the next note in the scale and so on...to find the whole scale on the neck?
[/quote]
The concept you are struggling to grasp is the issue of the scale formula. Do you understand what I have written above?
[QUOTE=Itsmesilly]Do all root notes start on the 5th and 6th string?

No. Any note, anywhere on the guitar (or any instrument) can be a root note. We simply use the 5th and 6th strings as convenient reference starting points for beginners.
[QUOTE=Itsmesilly]
The root note is what names the scale yes?

Not entirely.

The root note give the scale it's musical alphabet letter name:
C major scale

As opposed to C-sharp, D, D-sharp, D, etc.

The scale formula provides the type of scale:
C major scale

As opposed to minor, harmonic minor, melodic minor, etc.