The root management server (RMS) is the central point of configuration management and overall health monitoring for the entire managed environment.
The root management server encryption key holds all the Run As Account information defined in the management group. To successfully restore a failed root management server, you must use that key to reattach the databases and to access the Run As Accounts that have been encrypted with this key. If you need to restore the root management server without this backup, you need to re-enter your entire Run As Accounts.

Encryption Key Backup or Restore Wizard is open. Click Next to proceed.

Select the option Backup the Encryption Key.

Specify the location to backup and enter the file name.

Enter the password to protect the encryption key.

Backup Encryption key is completed. Click Finish to close the wizard

You've completed the installation of SCOM and backup encryption. To back up or to restore the root management server key, you need to use the SecureStorageBackup tool. The tool can start the Encryption Key Backup or Restore Wizard, or run as a command-line tool.
In the next upcoming article, i would look into verifying and post-configuration of SCOM installation.