Where is a good place to start understanding theory? I've been learning scales and memorizing their notes but I'm still lost as to how to learn theory. Where's a good place to start?
A good one that comes to mind would be that beginner's article on here about intervals that I read a while back. Hold on, I'll see if I can find it...

Ooh, then a good place to go from there would be Chord Progressions. [<--clicky for helpful article]

And then if you're still hungry for knowledge, be sure to check out the superb installment of articles from the wonderful SethMegadefan right here.

Those oughta get you a pretty broad spectrum of knowledge. Good luck with guitar playing!