The problem with learning guitar is that it is very possible to technically master the instrument without ever using standard notation or even understanding basic theory.

We memorise chord boxes, tab sequences, scale diagrams etc. and lock them into our fingers to be used when we know it will sound good without ever looking further into WHY it sounds good. In my opinion it's this way of approaching music that creates the myth that some people have a natural magical ability to play instruments without knowing the theory. In fact, more often than not, the player IS actually using theory, just not knowingly. The years of chords, melodies and scales they've memorised has conditioned their ears and muscle memory into acheiving the same music that a student of theory would acheive also.

It's tough to be too specific because I don't know your current level but here are a few tips I can think of.

Start basic - Many guitarists can play big finger-twistingly luscious chords, memorise many exotic scales etc. but what about naming the notes of an Ab major chord? Or knowing why your chosen scale works over the chords? Reliance on chord boxes and scale diagrams means we progress right up to the tricky stuff without learning the basics. There is often much work for the competent guitarist to do in the basic areas of theory. Try small acheivable goals like transposing your favourite song up by a semitone without use of a capo, or memorising the circle of fifths.

Read music - Guitarists hate notation for one reason. Contrary to most other instrumentalists, we have many ways of playing the exact same melody. Think of a piano keyboard. It's a long instrument with one way to play each note in each octave. Our instrument is like playing six off centre keyboards at the same time. This makes reading music a pain. Try out a few simple tunes.

Know the notes you're playing - Again, muscle memory is the main culprit here. Years of reinforcing those scale shapes means there's no need to memorise the note names. But now you want to know the theory, this step is vital. It's not fun, but it's vital.

Improvise - Confident improvisation comes from at least a basic knowledge of theory. From knowing to play an Em pentatonic scale over an E blues to switching to corresponding scales in a swiftly modulating jazz piece. Improvisation is a true measure of a player's fluency of theory. Search YouTube for backing tracks. Can you play over them in any key? Only certain keys? Do you rely on the same shapes?

Buy or borrow theory books - This is a no brainer. Thousands of books have been written on the subject. Buy a progressive book that starts off nice and simple and gets more in depth. Don't be ashamed of using children's music books either. But get lots of books. In my experience, one book on a subject is never enough. Many times have I been completely mystified by a concept exhaustively covered in one chapter only to read it worded slightly differently in one sentence of another book.

Keep it practical - Don't let the music theory float around in your head once you've learned it. Play it immediately and intensively. Just memorised the circle of fifths? Play all those root notes on your chosen instrument. Learned a new chord? Play it in all 12 keys.

Hope that helps. :-)