How to use JSF h:messages better?

The h:messages displays all messages, also the ones which are already displayed in a h:message in the page. You can however set it to only display messages with a null client ID using globalOnly="true".

<h:messages globalOnly="true" />

You can also give the message a different style depending on the FacesMessage.Severity:

<h:messages infoClass="info" errorClass="error" />

with for example this CSS which hides the INFO messages and makes ERROR messages red:

.info {
     display: none;
}
.error {
     color: red;
}

You can use redisplay="false" to tell it to not display the already displayed messages via e.e. <h:message>.

<h:messages redisplay="false" />

You only need to make sure it's placed in the component tree after all those other message components. You can if necessary make use of CSS to reposition it somewhere in top.

Just to be sure,

facesContext.addMessage("clientId",  facesMessage);

this will attach the given message to a <h:message for="clientId"> not to a <h:messages id="clientId"> as you seem to expect.

change <h:messages> to <h:message>

<h:messages displays all messages for the current context, <h:message> displays a specific message.

and I believe you want to change id to for to give it a target, but I could be wrong.