Yea, as mentioned in this post: [Support Guide] Understanding and using Netlify's API, the best way to learn how to use our API is to watch how our UI (app.netlify.com) does things. That said, I’m glad you found the info you needed in the js-client readme.
For those Personal Access Token, you can set those in an ‘Authorization’ header when invoking our API endpoints. The value will look like: Authorization: bearer <personal access token>
Hope that helps.