I think you'll still ultimately want to write by ear. To me, theory simply gives you a bigger musical vocabulary, a better understanding of how to put things together and a better way to communicate ideas.

Eventually you'll get comfortable with new stuff you're learning so that it becomes second nature. You probably won't want to consciously shoehorn some new thing you're learning into a song. It should feel as natural using the current musical vocabulary you have now.

I'm by no means an expert on music theory, but I managed pick up decent amount from reading and being around good musicians. It sounds like you're looking for the fast track to figuring it out. Don't expect it to be as simple as you'd hope. I've seen a lot of guitarists (myself included) who memorize all the chords in a Mel Bay book and learn some scales thinking they've conquered music theory. This is the example I think of when people talk about the Dunning-Kruger effect. Watching somebody arrange parts for an orchestra can be a humbling experience. That said, there are a few particular things that have helped me a lot:

*Learning to use proper voice leading for both chord progressions and for arranging harmonies

*Learning how different types of modulation work and how to use them.

*Finding uses for "weird" or dissonant chords that have no immediately apparent use. Something like a half-diminished seventh chord may sound ugly out of the context of a song, but they can be exactly what you were looking to transition between two other chords. This is the sort of thing I tend to learn by example.

*Learning how to use borrowed chords

*Analyzing songs that do something interesting and then trying to pinpoint what it is and why it works. In addition giving you a better understanding of the music, it will help expand your bag of tricks and add more variety and character to songs. Sometimes you may need to ask somebody who knows theory because you can't exactly google a musical concept.

This is all assuming you already have a decent grasp of the basics. You obviously need to know what different chords are called, basic scales and general music terminology before diving in.