Of all the different parts, systems, and components on your bike, the one you're probably the most apprehensive about working on is your transmission. There's a lot that goes into your bike's transmission, but don't let that make you think it's impossible for you to understand. With a little work and brainpower, you can figure it out just like you can with anything on your bike.
As you probably know from the other posts on Wind Burned Eyes, I'm a big fan of the MC Garage video series from the guys over at Motorcyclist Magazine. Here's a excellent video giving you a basic rundown of how a motorcycle transmission works. While it won't make you a transmission expert, it will show you the inner workings of a transmission and explain how things go together.