With access to the server's crontab, the command-line script makes a backup on a schedule. The Backups > Settings page shows the line for your server. For a backup every night at 2:00, add to the crontab of the web server's user (for example crontab -e -u www-data):
0 2 * * * php /var/www/omeka/plugins/Backup/bin/backup.php create >> /var/log/omeka-backup.log 2>&1
Use the path of your PHP command-line binary (which php) if php is not on the cron user's path. Run it as the web server's user, so the archives can be read and deleted from the admin.
After each backup, older backups made on the site beyond the number in Backups to keep are deleted. Uploaded, downloaded and copied-in archives are kept.
Scheduled backups appear in the list like any other. To keep a copy off the server, download them, or copy the backup directory elsewhere with your usual tools (rsync, a backup service).