To Close the thread, We just need to use the MOMCertImport.exe tool to load the certificate into the SCOM agent which in turn update the registry settings. Once imported. you will see the Channel Certificate Serial Number.
do a reg query for the below path:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft Operations Manager\3.0\Machine Settings
now you will see the Cert details in the SCOM Management Pack ( https://github.com/thekevinholman/SCOM.Management ). You can download the mgmt pack from Kevin Holman's github site.