You just need to stop the SEPM service on both to do the upgrade. The installer is smart enough to know that DB schema is already upgraded and doesn't need to do it.
See here for the details:
Replication in 12.1 and later
For SEP 11, you had to break replication between SEPMs by deleting replication partners before perform a SEPM upgrade. Failure to break replication could result in corrupt databases. SEP 11 replication did not perform version checking. SEP 12.1 and later prevents the need to disable replication prior to upgrade. Starting with SEP 12.1, replication performs version checking, and eliminates cross-version replication corruption.
Note: When you upgrade from SEP 11 to SEP 12.1, you must still break replication.
http://www.symantec.com/docs/TECH160642