Hello,
In your case, you would be migrating the server OS as well as SEP 11.x to SEP 12.1.
Check these Threads which speaks on the same issue -
https://www-secure.symantec.com/connect/forums/symantec-1106-121-migration-question
https://www-secure.symantec.com/connect/forums/migrating-sep-11-old-hardware-sep-12-new-server-hyper-v-vm
In your case - there are 2 scenarios -
1. Upgrade the SEPM 11.x on the existing 2k8 32 bit server to SEP 12.1, then move the installation to the new 2k8 64 bit server by performing a disaster recovery.
How to move Symantec Endpoint Protection Manager 12.1 from one machine to another
http://www.symantec.com/docs/TECH171767
Symantec Endpoint Protection 12.1: Best Practices for Disaster Recovery with the Symantec Endpoint Protection Manager
http://www.symantec.com/business/support/index?page=content&id=TECH160736
OR
2. Move the installation of SEPM 11.x from the existing 2k8 32 bit server to the new 2k8 64 bit server, then upgrade it to SEP 12.1 after it's moved.
How to move Symantec Endpoint Protection Manager from one machine to another
http://www.symantec.com/docs/TECH104389
How to point clients to a new SEPM after decommissioning or replacing the primary SEPM.
http://www.symantec.com/docs/TECH92556
Migrating from Symantec Endpoint Protection v.11.x clients to Install Symantec Endpoint Protection v.12.1. could migrate flawlessly without any issues.
It is always recommended to perform a Disaster Recovery for SEPM 11.x before Migrating to SEP 12.1 as a Backup step.
Here are the Best Practices for Upgrading to SEP 12.1 RU2 -
Best practices for upgrading to Symantec Endpoint Protection 12.1.2
http://www.symantec.com/docs/TECH163700
Also, check the Articles for the Migration on :
Quick Access to Symantec Knowledgebase Articles of Symantec Endpoint Protection 12.1
https://www-secure.symantec.com/connect/articles/quick-access-symantec-knowledgebase-articles-symantec-endpoint-protection-121
SEP 11.x to SEP 12.1 Upgrade process graphical overview
https://www-secure.symantec.com/connect/articles/sep-11x-sep-121-upgrade-process-graphical-overview
WhitePaper for Migration: https://www-secure.symantec.com/connect/downloads/migration-whitepaper-symantec-endpoint-protection-version-121
Hope that helps!!