Well, there are probably as many ways of homeschooling as there are homeschoolers :-) but here are some of the main models:
School at home - This is where you read the books, do x amount of worksheets, and call it a day. This is usually the most comfortable method for new homeschoolers.
Classical - There are two methods of this - Greek/Roman Classical and Hebrew Classical. Both are based on the same model, but have different philosophies. Greek/Roman is very much based on knowledge for the sake of knowledge (as their culture was based on education in order to gain knowledge or further the strength of the state). Hebrew is more based on truly reaching the heart of your child in order to help them understand their world, their place in it, and their religious beliefs. Both lend themselves well to worldview studies on the middle and high school levels. Greek/Roman can be either secular or Christian, Hebrew tends to include Christianity or Judaism fairly heavily. Here are some sites:
Greek/Roman:
http://www.classical-homeschooling.org/
http://www.classicalhomeschooling.com/
http://www.homeschool.com/Approaches/Classical.asp
Hebrew:
http://heartofwisdom.com/
http://www.triviumpursuit.com/index.php
Unit Studies - This is where pretty much everything you do is based around a common concept or theme. Take, for example, ocean predators: you can read about them (reading and comprehension), research and write a report on them (language arts and writing), perform experiments to show how a shark moves so quickly through the water or how the tentacles of an octopus suction onto their prey, or how different animals use advertisement and camouflage to stay safe (science); you can research a couple of famous marine biologists and their discoveries (history, language arts); you can make word problems based on the animals and their environment (math); you can research the different layers of the ocean, what their characteristics are, and what animals live there and why (science, language arts); you can do artwork based on the different animals, the biome, the plant life, etc. (art, science); you can find and analyze/memorize poetry based on different aspects of the ocean and the marine life (poetry, literature); you can do a study of the different layers and how they affect life (geography); and the list goes on and on. Here are some sites that give info on unit studies:
http://konos.com/
http://unitstudy.com/
http://unitstudies.com/default.aspx
http://almaproject.dpsk12.org/unitlist.htm
http://clepprep.tripod.com/cleplessonplans/
http://edsitement.neh.gov/
http://www.eduplace.com/monthlytheme/
http://homeschooling.gomilpitas.com/
Charlotte Mason - this is very literature-rich homeschooling, and in its truest form is very structured. It is also done in a looser, close to unit-study type of format. It is based on the trivium (like classical homeschooling) but generally has short (20-30 minute) class periods and plenty of extras. Here are some sites to give you info:
http://www.charlottemason.com/
http://sites.silaspartners.com/cmason
http://amblesideonline.org/CM/toc.html
http://www.amblesideonline.org/ (free K-12 curriculum for CM)
http://homepage.bushnell.net/~peanuts/faq1.html
Eclectic - This method combines a bit of everything to tailor a curriculum specifically for your child. If your child needs a very structured math curriculum but is a voracious reader and creative artist, likes hands-on science experiment but likes to notebook and timeline through history, this is for you. It's just what it sounds like - pieces of everything. Here are some sites:
http://eho.org/
http://members.aol.com/clayvessel/
http://www.educationalfreedom.com/heart/pages/eclectic.html
Unschooling - this method allows the child to study at their level and according to their interests, but allows the child to choose their own studies. The parents act more as facilitators, supplying their kids with the opportunities and resources, helping them to locate answers when necessary, but otherwise letting them go to learn. This works very well with a motivated student and a confident mom; there are unschooled kids that have gone on to become CEO's of very successful businesses, etc. However, if you have a child that is unmotivated to learn, or is not at all confident about searching out information, this may not be a good idea. Here are some sites:
http://www.unschooling.com/
http://www.unschooling.org/
http://www.unschooling.info/
http://www.home-educate.com/unschooling/
http://www.naturalchild.com/guest/earl_stevens.html
Homeschoolers use any and all of these, or even a combination of two or more. You have the freedom to use whichever you would like, based on your free time and teaching style, as well as your student's learning style. You will most likely find that your methods develop over time, as both you and your son become more comfortable with homeschooling and his abilities develop. And it's fine to do that!
Hope that helps :-)
Edit...I just realized I didn't put down what we do! Sorry about that. We're pretty eclectic.
Math: Math U See, which is taught by DVD and very concept and manipulative based.
Language Arts: Learning Language Arts Through Literature, a workbook that interrelates all areas of LA and ties them into literature.
Bible: We do a family Bible study every night, and he reads a specific amount each day. He also does tons in his AWANA books and studies up further on anything that interests him. He also takes an OT History/Biblical Feasts class at co op.
Science: We use Apologia, he goes through about 2 elementary texts per year. He's starting 5th grade right now, will be moving into the jr. high program sometime next spring. We also do unit studies whenever the interest pops up.
History: We use both a textbook and a lapbook/notebook/hands-on study for history. We're in American History right now, so we're using All American History, which he does pretty much by himself. He also reads historical fiction and biographies at grade level. We then do a study either from http://www.handsofachild.com/2/ or http://www.homeschoolinthewoods.com/ to get more into it and nail down the ideas, people, places, events, etc. We keep a general timeline in his notebook, and he does a specific timeline in his notebook or lapbook with each event that we study.
Writing: IEW, which is integrated with his other subjects (generally Bible, science, and/or history.)
Spanish: The Easy Spanish
Greek: Elementary Greek
Geography: Right now we use continent and studies from http://www.handsofachild.com/2/, we will be moving into a more literature and research-based format next year. We also integrate geography with history.
I think that's it...other than that we read, cook, go on field trips, make projects, and discuss. He thinks it's fun, and he learns tons!