[doc] Modified the organization of the overview section and tried to make the section on the API configurations clearer.

I made the following changes to the README:

- Reorganized the overview to have more of a hierarchical structure.
- Rewrote some of the paragraphs explaining the API configurations/defaults and app settings, which I found confusing. Please review this section before merging PR. 
- Made copy edits.

**Note:** I think the "Example" section should eventually be "Examples" and have subsections for "Basic" and "More Advanced". The more advanced example should show how to attach string properties on `app.locals` and `res.locals`, give examples of app settings, and then display the values with the `toString()` method.