If you look into some articles in guitar magazines like guitarplayer or sometimes musiciansfriend, you might be able to pry some info out. You can always try googling and get information that way. Seymour Duncan has a page about some of the basics, it gives decent information about some of parts that really affect tone and how different pickups can be paired with different set-ups to achieve a desired sound. That might help a bit.
Duncan Designed - Seymour Duncan/Basslines At the top, Support: Choosing and Installing: How to Pick a Pickup. Its more oriented around how pickups work but its something. My best advice is play guitars a lot of different kinds of guitars and ask what they're made of and what they're equipped with. Then maybe you'll discover that wood type A tends to give me a sound that I like. Then you can research a bit on the wood and find out that the unique tones are accentuated with pickup type A and muddled with pickup type B. From there, it just keeps going. I started with an Epiphone SG and added new pickups and got exactly what I was looking for. I'm currently reading up on a Jackson Dinky and trying to determine which pickup will give me the sound I'm looking for. I would try to look through some copies of GutiarPlayer, you might find stuff you like, and maybe it would be worth subscribing to. I still have a few copies around that talks about different pedal setups.
Which leads to a tidbit of info, remember that the sound is not all about the pickups. They work with different types of would, the design/shape of the guitar, hardware, and even wiring to the amp. 10 ft cable vs 100 ft cable makes big difference. If you ever start playing with pedals, keep in mind that even things as pedal order can change the tone. I find that if I order my distortions/overdrives one way, the tone is too sharp and trebley, but by changing two pedals, it balances back out and sounds great.
I'm just wondering, why do you ask about how everything works together to produce the sound, other than curiosity? Are you buying a guitar or making/ having a guitar made. If you are buying one, just ask about the specs on guitars that you find sound good, then find one that plays the way you like, made of similar parts, and sounds similar/to your liking. If your making one, then hmmm... Not sure what to tell you. Don't rush it, think carefully. My friend has been doing this for about 5 years or so. His work is amazing but he is always surprised with how the guitar will sound.