Please be aware that the "Full Backup" and "Account Backups" in the Backups section of CPanel do not contain the Home Directory (and the public_html directory within).
This has been done to reduce server load.
We have "Full Site" backups stored elsewhere which can be requested at any time for free.
To get a complete backup of your site through the CPanel Backups interface please download the "Full Site Backup" which will contain your databases and other files related to CPanel. Then, to get your website files, email, and stats please use the "Download a Home Directory Backup" link.
If you want to backup only part of your website files the "Compress" and "Extract" features in CPanel File Manager may be helpful for zipping and downloading folders.