Godot allows for a great amount of flexibility in how you structure a project's codebase and break it down into scenes. Each approach has its pros and cons, and they can be hard to weigh until you've worked with the engine for long enough.
You should start by reading Applying object-oriented principles in Godot. It explains how Godot's nodes and scenes relate to classes and objects in other Object-Oriented programming languages. It will help you make sense of the rest of the series.