Okay so Im just delving into the world of theory after 3 and a bit years of playing. I know basic chord theory and know inversions and I know a few scales, but my problem is my hands know where to play but I dont know why it works, if you get what I mean.

So uh.. yeah. What such I focus my attention to next?
What are your goals? We can't point you in the right direction if we don't know your destination.
I think it is worth your time to look at the many lessons on ultimate-guitar.com. It can be really overwhelming when you try to tackle all of music in one go.