If you wish to maintain the configuration and logs:
While it is possible to perform a SEPM move and upgrade simultaneously (in my testing, you must be using sql db, and should maintain same name/IP address of SEPM), it is not recommended and unlikely to be supported by Symantec should you encounter any issues.
The recommended procedure is to perform the move and the upgrade as two separate tasks. The order in which you perform them is not important, merely that you only move onto the next task once the first is complete and verified as working. Please see articles provided by admin_sepm ("Thumbs Up" BTW).
If you don't want the old configuration and logs:
If you don't mind losing the old logs and configuring everything in the SEPM again (settings, policies, group structure, reports, etc), then you could just setup the SEP12.1 server as a new, independant installation, and move clients across to it using the Client Deployment Wizard:
http://www.symantec.com/docs/HOWTO81109