I see what a prefold is...but how do I fold it?

It's not as complicated as you may think! The easiest way to use a prefold is fold longways in thirds and lay it in the cover. There are more ways to fold, check the links below, and you can use pins or a Snappi, or just fasten the cover.

SNAPPI tutorial - Never use a pin again!

Diaper Folds for Prefold and Flat Diapers
Folding a cloth diaper using a wrap (animated)
Folding a cloth diaper (animated)
Night Time Double
Diaper Folding 101
THE ANCIENT ART OF DIAPER FOLDING
Folding
Folding a Prefold
The Nappy Lady - Article
How to use cloth diapers
ClothDiaperFolds.pdf
Folding Instructions
Super trim fit
Diva Fold

What's the difference between different kinds of prefolds?

Personal preference, really. Some think Indians or Europeans are softer, while Chinese absorb more. There are also hemp or bamboo.