This article is for cPanel Accounts. Determine where your account is with this guide.
You will need to upload your site files to the public_html folder. The www folder is a symbolic link so you can also upload through that shortcut.
If you are uploading files for an Addon domain you want to make sure you upload to the location where you pointed that Addon domain, which is usually public_html/addondomain.com
If you delete the public_html or www folders you may receive a 404 error when you try to connect in a browser.