Your main domain loads from public_html. A file at public_html/index.html is what a visitor sees at yourdomain.com.
Addon domains get their own folder, normally public_html/addondomain.com, and subdomains work the same way.
Anything you place above public_html is not reachable from the web. That is the right home for configuration files, credentials and anything else that should never be downloadable.
Two things that catch people out: your home page must be named index.html or index.php, and file names are case sensitive, so Logo.PNG and logo.png are different files.
