You can add your Listener for Monitoring. by following steps..
On EM go to Agent Home page (Agent target will be like hostnameort)
for the node where Listener is running.
from Add combo box select Listener and click go.
It will ask you few details like
1) what Name you want to give to target.
and few more.
Just go through next next and Monitor your Listener
Can you post the full output of
$emctl status agent
Also, Check the $ORACLE_HOME/sysman/config/emd.properties file for hostnames/port etc. Then check the targets.xml file to see if you see any targets. Else the same directory of targets.xml should have a trace file (.trc) with some error.