The Developer Tutorials website has posted an article with a sort of beginner's guide to working with WordPress and its customization.

WordPress is a state-of-the-art semantic personal publishing platform with a focus on aesthetics, web standards, and usability. [...] WordPress is what you use when you want to work with your blogging software, not fight it.

They briefly mention how to use the administrative interface for the tool, but focus mainly on the templating system. They talk about the structure of the themes and how to create your own inside it. There's even parts detailing the specific sections (like the header, the posts section and the sidebars).