Hi Francesco,
sorry for the late response. I will try to clarify your situation.
Manager
First of all you manager ossec.conf is only for your manager, it doesn't have any effects on your agent's.
Agent
Now on your agent you have the ossec.conf only for the agent.
Centralized
If you want to override the agents configuration, you can do it by editing the file
/var/ossec/etc/shared/default/agent.conf on your
manager. This will generated a
merged.mg that will be pushed to all the agents connected to the manager.
After the agent receives the
merged.mg file, it will uncompress it and generate the
agent.conf.
The agent will restart, read it's own ossec.conf and override the options with the agent.conf received in the previous step.