To clarify, the SEPM services must be stopped on ALL SEPMs in the same site (i.e. sharing the same DB) prior to the upgrade anyway.
This means that after the upgrade of your passive SEPM to RU5, it should be the only one with running services, and therefore the only one clients can connect to. This means just logging into it should show you whether or not things are working.
If all's cool, shut down the services on the passive SEPM (so that, again, services are stopped on all SEPMs) and upgrade the primary. Once done, log in and check if clients are checking in, the startup the services on the passive SEPM (as they'll both be on the same version at this point).
Replicating SEPM environments are slightly different. Can you provide more info on the estate you're upgrading?