One method is to unzip your file to a folder on your desktop, and then ftp the folders and files into your root (usually public_html). If you have had a virus then it is recommended to delete the original files and folders first. If not you can just select to overwrite them. My plugin includes the sql database backup in the zip folder, and that file needs to be restored through phpmyadmin in the cPanel.
http://codex.wordpress.org/Restoring_Your_Database_From_Backup