1) Do SEP 12.1 install and SEPM 12.1 install is different or the same?
SEP is the client and SEPM is Symantec Endpoint Protection Manager Console which is the console through which you can manager SEP clients, which is the actual antivirus.
2) how the 11.0 remote agent will work with new installed SEP?
SEPM 12.1 can fully manage 11.x Clients and they would continue to communicate with the 12.1 SEPM
3) Do I have to update the sylink.xml files on the remote computer manually
Yes, Since you would have to..you could either use the Sylink Replacer Utility or the Sylink Drop.
You would be able to get these tools by contacting support and opening a technical case.
4) do I have to uninstall them from all the clients and then push the remote agent from SEP server again
No, you can just update the sylink on the 11.x clients and then follow the upgrade process to upgrade your clients.
Once your clients start communicating, things are much simpler.
Installation and Migration Documents for Symantec Endpoint Protection 12.1
http://www.symantec.com/business/support/index?page=content&id=TECH163707&key=54619
Phone numbers to contact Tech Support:-
Regional Support Telephone Numbers:
United States: https://support.broadcom.com (407-357-7600 from outside the United States)
Australia: 1300 365510 (+61 2 8220 7111 from outside Australia)
United Kingdom: +44 (0) 870 606 6000
India: Toll-Free 000 800 4401 456 directly
IDD call: +61 2 8220 7111
Additional contact numbers: http://www.symantec.com/business/support/contact_techsupp_static.jsp