Ok so I understand the whole concept of scales and chord formations theoretically but on guitar I'm confused in the way to go about learning them. Because for example let's look at Am Pentatonic. I'm really confused as to how to learn them. Like I know the patterns to it but lets take the shape starting on the 3rd fret. The root is the A on the 5th fret, low E, but the G on the 3rd is still in the pattern. Should I learn the scale from A to A and just know that the G is there for when I'm doing a quick descent improv or what, because if I start on G then technically isn't it a different mode? This issue also confuses me on relative majors and minors, like besides knowing the different sound, whats the use in learning Cmaj vs. Am when you are just soloing? If someone kinda gets what I'm saying please help me.
.... So what are you asking? All you've said so far is... Well who knows. Could you be more... "specific"?
I'm just unsure as to how to learn scales. Like should I know the Am Pentatonic scale as A to A or the entire box kinda I guess. I just figured the box from G to A would be like a diffferent mode or something.
nah man, the start of the position has nothing to do with what mode it's in. Am pentatonic covers the entire fretboard, it's the backing instruments and the way that you move through the notes that sets the root tone. tough to explain, but if you have a bassist playing A and you start with a G, you're not changing modes unless you end and put special emphasis on the G.. check up on phrasing, because if you understand the theory, then it's phrasing technique you're having difficulties with. hope that helped.
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Try not to think in terms of patterns too much. A scale is a set of notes, not a pattern on the fretboard.

A minor pentatonic is A C D E G. So when you play these notes you are playing in Am pentatonic. There are things that can change this, but I won't go into those. The chords also play a role in what scale you are playing.
Ok so I think I get what is going on but one last thing is since I'm just memorizing the pattern which has notes outside of the octave should I memorize the roots(prolly redundant but I'm really afraid I'm not grasping this)?