In the Backups tab, 'Take Backup' snapshots your server anytime. A backup covers worlds, plugins and configuration, compressed and integrity-checked. Without File Protection you can keep up to 2 manual backups; with File Protection you can take unlimited manual backups.
With File Protection enabled, the system takes an automatic backup every day the server is running; the last 7 automatic backups are kept and older ones are pruned automatically. Your manual backups are unaffected and all remain.
To restore, pick a backup and click 'Restore'. The server is briefly stopped, files are rolled back and it restarts automatically.
Backups are stored independently of the server: even if you delete the server you can still download them.