All files that you want to appear on your website should be uploaded to within your public_html folder. This can be done so via a FTP client, or via the cPanel File Manager:

Firstly click on the public_html folder as outlined below to be sure you are inside the public_html:

Then click the upload button to start adding files to your site:

You can also upload files above your public_html folder, these will not be accessible via your website.