I am in the process of upgrading to OEM 12c using the 2-System method and I am slowly making progress. Using the OEM 12c Upgrade Console I was able to get the Deploymnet/Configuration step to succeed but the Check Agent Readiness Step failed. I found the error in the <Agent_Instance_Home>/sysman/log/gcagent.log file on the target machine - ORA-12505, TNS:listener does not currently know of SID given in connect descriptor.
Once I resolve that is it simply a matter of going to the Upgrade Console -> Deploy and Configure Agents page, select the cleanup failed deployments tab and go from there or is there something else I must do. I haven't been able to find specific instructions on how to proceed in such a situation.
Yes your understanding is correct, just slect the option " cleanup failed deployments " while doing the agent deployment and it will take care of everything.
I also see that you have posted few queries in the forum about EM upgrade , i suggest you open an SR with oracle support , so that they can guide you through the upgrade process and help you in case of any issues. In case you have already opened an SR with support then pls ignore this suggestion. :)