I know there a few different methods of learning the Major Scale all along the neck:
CAGED Method
3nps Method
Modes and the positons

I have been practicing all three but Im wondering if these methods have different applications. Like I hear people saying "playing in position" so I a assuming they mean using the modes and postions method to play that style.

I have been learning all three methods im just wondering what you guys think about them and which method (if any) would be better used for connecting the scales when trying to solo up and down the neck.. any input will be appreciated
First, learn how to play the scale along a single string by following the WWHWWWH note formula. After that you can add more strings until your playing all over the neck. Just start at the root note and follow the formula. W= whole step or two frets, H=half step or one fret. When going from one string to the next a whole step is equal to 4 frets and a half step is equal to 3.

Ex. Gmaj scale- the fifth fret on the low e string(A note) to the second fret on the a string(B note) is a whole step interval.
The application is simple - it's a way of organising your note choice. More ways = better.

Do you understand where these positions are derived from? Figuring this stuff out yourself is great.