I'm having trouble trying to write a song where there are two or three guitars doing their own thing, but it still works out in the end. Usually what I do is try to listen to a band that does what I'm working on to try and get some ideas/inspiration...but my ears aren't good enough to pick up the discrepancies between the guitars.

Does anyone here have advice for doing so? The band I'm listening to a lot right now that does that is Bedhead. They're a cool band and I've gotten a tone of ideas from them, but I have trouble trying to get that three-guitar goodness.
read up on counterpoint and steal some of the principles. i haven't formally studied counterpoint, but incorporating ideas like avoiding big interval leaps per voice, landing on consonant harmonies on the strong beats (and the option to land on dissonance on weak beats), you will have good guidelines to start experimenting off of.

learning the sounds of more complex chords (7ths, extensions, suspensions), when they fit in a progression, and more importantly which ones you like, is also very helpful. because having several different voices is essentially the same as playing lots of moving chords. if you learn these sounds, your ear will also be able to pick them up more easily when you're trying to analyze a song.
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The Study of Counterpoint is a good book on the subject. Practicing the exercises will get you familiar with some of the basic 'rules' that make for what is generally considered good counterpoint. Feel free to break them though. Polyphony is all about maintaining the uniqueness/independence of the line.
Awesome, thanks for the suggestions. I'll check that book out for sure, do you think it'll be at a bookstore? The one I go to sometimes has guitar related books, but it's usually more beginner to intermediate stuff like "nirvana tab" or "led zeppelin tab" or "introduction to pentatonic scales"...stuff like that.
If I were you I'd just pick it up off of amazon. It is Fux's Gradus Ad Parnassum translated into english and I think you'll be hard pressed to find it in your typical bookstore or music store.
You'll need to be pretty well versed in traditional harmony and counterpoint before you can come up with good polyphany.

For listening and analysis, you can't go wrong with Bach. Start with something basic like his 2 Part Inventions.
I don't think trying to learn a more standard classical approach to counterpoint/polyphony is going to help you. You're most likely going to write something entirely different anyway. Just try to listen/play/analyze other bands who use multiple parts, for example Gordian Knot, Cynic or Scale the Summit.