Just follow Setup --> Add Targets --> Add Targets Manually.
Now you can follow the steps, select host etc.
The Container database and the PDB's come up nicely in Cloud Control:
Note that the Container Database is clearly mentioned. If you click the little arrow icon, you get the PDB list:
This opens up the PDB screen:
During Configuration you will need to set the password for monitoring (default the DBSNMP user). This user is defined on containerlevel, so it doesn't really matter if you set (or reset) the password on CDB or PDB.