To Start enterprise manager 12c you need to follow the below steps :

export ORACLE_HOME=/u01/app/oracle/product/11.2.0/dbhome_1
export OMS_HOME=/u03/app/oracle/Middleware/om12c/oms/
export AGENT_HOME=/u03/app/oracle/Middleware/agent12c/agent_inst/

• ensure database and listener is running
• Run the below command from $OMS_HOME

emctl start oms

• Run the below command from $AGENT_HOME

emctl start agent 

to Stop all the services you need to do the below :

 export ORACLE_HOME=/u01/app/oracle/product/11.2.0/dbhome_1
export OMS_HOME=/u03/app/oracle/Middleware/om12c/oms/
export AGENT_HOME=/u03/app/oracle/Middleware/agent12c/agent_inst/

• Run the below command from $OMS_HOME

emctl stop oms -all

• Run the below command from $AGENT_HOME

emctl stop agent 

• Now you can shutdown database and listener.

Thank you
Osama mustafa