To back up your Secret Server Installation use the following steps. ( Your Secret Server instance may be running during this procedure )
1. Navigate to the directory where Secret Server is installed and copy the folder (holding the application) to your back up location.
2. Open your SQL Server Management Studio.
3. Right click the database your Secret Server is running on, select tasks, then backup.
4. Click the Add button, you will be prompted to enter a file path. Make sure SQL Server has permissions for this location.
5. Copy the resulting database backup file to your backup location.
Note: You can also automate steps 2-4 by using the Command:
osql -S myserver\SQLEXPRESS -E - Q "BACKUP DATABASE SECRETSERVER TO DISK = 'c:\backup\ss.bak' "