Your account has both non-web accessible space and of course web accessible space. Your user home directory, /home/USERNAME, contains many files used to operate your website. You can create new folders here to store data or information you do not want the world to know about or see. This is a good place to store database connection or other files that contain passwords or critical data.
To upload your "homepage" or website materials, the stuff you actually want the world to see, upload into the "public_html" directory. You can of course create other sub directories and files there as well which will all be web accessible.
/public_html - This is where your site files will go
/public_ftp - Files for your anonymous FTP
/www - same as your public_html directory
Warning - Do not delete any pre-existing files or folders you first see in your home directory.