Hello,
In your case, you would not be able to merge 2 different databases until 1 of them is specifically installed for Replication.
In your Case, what is happening is, you have 2 SEPM's version 12.1 and both are created as "Install as My first Site".
So, SEPM 1 and SEPM 2 both cannot be replicated.
However, in your case what you could try is:
You would have to get all the Clients from SEPM 2 to report to SEPM 1 with the help of SylinkReplacer utility.
Once, all the Clients from SEPM 2 start Reporting to the SEPM 1. You can later uninstall SEPM 2 and Install SEPM 2 with "Install as an Additional Site" and set the Replication.
Now, since you are carrying SEPM 12.1 now, you may have to contact Symantec Technical Support for SylinkReplacer 12.1
For Replication between 2 SEPM 12.1, check this: http://www.symantec.com/docs/HOWTO55322
Hope this helps!!!