The File Backup has a couple of configuration options, outlined in detail in the Settings area, but the highlights are:
To execute the automated backup you'll, basically, be hitting a URL on a schedule. You can get the specific URL (and example command) for your system from the Cron Backup settings page. Automated backups can be configured to attach the backup to a notification email, customize the notification email, and who the notification email should be sent to upon a successful backup.
To take a file backup manually you have 2 options; from within the Backup Pro module itself or by selecting Backup Files from the Tools menu. When you initially get to the Backup Files page, you'll have to click Start Backup to begin the process.