The following are steps outlined are to be done initially when upgrading from SEP11.x to SEP12.1
Note:  The KB article does not go into specific detail on the migration steps, but the important steps that should be done before hand.
 

Before upgrading to Symantec Endpoint Protection 12.1 RU1, please read the Release Notes, as there are known impacting issues resolved in this release.

http://www.symantec.com/business/support/index?page=content&id=TECH174565

New fixes and features in SEP 12.1 Release Update 1 (RU1) 

Step 1) Upgrade Serial Number.

To upgrade your serial number, go to Symantec Licensing Portal:

https://licensing.symantec.com

Log in or register, and upgrade your license serial number to a 12.1 license number.
More information about upgrading your serial number can be found here: 
http://www.symantec.com/docs/HOWTO56030

How to upgrade your SEP11 license to SEP12.1 online

Alternatively, this can be done by contacting Symantec Customer Care, quoting your old serial number.

Step 2) Download Installation Package:

Go to FileConnect: https://fileconnect.symantec.com
 
- Select your language and login with the new serial number.
- Read and accept 'Terms and Conditions'.
- Click on the folder related to your installation language.
- Download the file for the installation of Symantec Endpoint Protection:
 
For example:   The file is called "Symantec_Endpoint_Protection_12.1_RU1_Part1_Installation_EN.exe" for International English.

Please Note! You can only upgrade with a version in the same language as the version currently installed on your system.
 
When the download is complete, double click the file to extract it. Choose or create a temporary folder for the installation files and folders.
NOTE: Ensure that there is a reasonable amount of disk space to perform the upgrade.

 
Step 3) Disaster Recovery
 
Perform the Disaster Recovery as per document:
http://www.symantec.com/business/support/index?page=content&id=TECH102333

SEP 11.x:  Best Practices for Disaster Recovery with the SEPM
 
Step 4) Installation of Symantec Endpoint Protection Manager (SEPM).
 
The guided procedure will detect and upgrade the Symantec Endpoint Protection Manager installation on your system.

Important:  Before starting the upgrade process, stop the "Symantec Endpoint Protection Manager" Service.
 
In the Configuration Wizard, just confirm the current settings. When upgrading a SEPM that uses a SQL database, insure that you have sa-level credentials to authenticate to the SQL database for the migration process. The database must also be specified in the serverName\instance format.
Please note that this process can take a long time, depending on machine workload, client numbers and environment complexity. Do not interrupt the upgrade process.
 
Step 5) Upgrade Client Packages.
 
Warning! The SEP client package version 12.1 is not compatible with Windows 2000. If you have machines running windows 2000, it is recommended that the package version 11.x is left installed, where it is still possible to control these SEP 11.x clients from the new SEPM console. Generally, it is good practice to create a separate group for legacy clients.
 
When the SEPM upgrade is completed successfully:

- Open the SEPM Console and go to the Admin section.
- Select “Installation packages” from the list of items.
- In the Tasks, click "Upgrade client with package".
 
Use the wizard to select the package version 12.1 and apply it to the group that is to be upgraded.
Repeat the procedure for the groups where deploying the package is required.