There's a metric megaton of stuff online about scales, scale theory and what works with what. The difficulty you're going to have with online, mostly free, stuff is quality control, as some online contributors explain simple things in an unnecessarily complex fashion, and some aren't any good at explaining the advanced stuff.
Being old enough to have started learning without the aid (or distraction) of the World Wide Tubes, I started out with "The Guitar Case Chord Book" and shortly thereafter "The Guitar Case Scale Book" (sadly I can't say who the publishers are because I've leant them to a friend), which I'm sure would still be in print. They're no-nonsense but they are rather clinical, and I did, for many years, harbour the honest hope that the Scale Book would enable me to unlock some kind of "key" to music and my understanding of it... no such hope: I ended up spending far too long thinking about WHY scales are they way they are, without ever working it out, until I realised that they just ARE and I should just get on with learning them.
If I were you I'd start with learning your standard 2 octave major, harmonic and melodic minors, and pentatonics of the same. If you understand the CAGED system start in the E shape, then the A shape, then the D shape. G shape is easy because it's just below the E shape (same root notes) and C shape is just above the D shape. Pay attention not so much to the notes themselves (we're guitarists) as the intervals: the intervals will help you with your chord theory... as in helping you with what makes (in basic terms) a major, or minor, or non-specific (like power chord where major or minor isn't explicit) chord. After that you can start picking up why a Gmaj7 is called that, and what the devil an F/B#sus4 might be... once you get the hang of it you start getting "EUREKA" moments as something you knew about but didn't understand suddenly become clear to you.
Scales are fundamental to all music and are a pre-requisite for a decent guitarist. The reason most guitarists start out with chords is because you only have to learn 3 of them to do a CCR number. In fact, if you can play Dm you can pretty much handle the whole of Run Through The Jungle. I digress.
If you don't go for a decent book to help you out then check out:
http://www.ultimate-guitar.com/lessons/
http://www.seymourduncan.com/blog/
I'm sure there's millions more, and the Ultimate Guitar one some of the articles are poorly written in that the writer seems to know what he's talking about but explains it badly. The Seymour Duncan Blog has some great "snippet" type lessons. Don't be alarmed by articles that have "Chord Substitutions" or "Inversions" in the titles: invariably they'll dip into scale theory to explain why it is the way it is, and that's always good for background knowledge... even if you don't understand it the first time, if you stick with it then one day you will, and you'll have one of those "EUREKA" moments that enriches your life forever.
It's worth it, is what I'm saying.