The docs have a useful links page with tutorials and courses from intro to more advanced topics. You can start there.
As for best practices, you should just stick with a blend of what you’re already comfortable with and with what the tutorials use. You’re already undertaking a big task by picking up Three.js, I wouldn’t recommend making your learning curve more difficult by adding more moving parts. You don’t want to spend a day debugging a bundler config file when you could be making progress on the course.