WordPress has lots of moving pieces, and it's crucial to understand how they fit together. This section tackles that topic:
WordPress Hooks, Actions, and Filters: What They Do and How They Work explains WordPress's hooks system.
Understanding and Using WordPress Child Themes explains WordPress's child theme system, what it's used for, and how child themes communicate with their parent themes.
Of the topics in this section, pay particular attention to the first chapter, on hooks, actions, and filters. They're really WordPress's way of allowing new code in, and they're crucial to almost everything you'll do in theme and plugin development.