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I already have an enterprise Java EE application. I want expose some of the existing EJBs as web services.
I wanted to know how to organize the Java EE project. I mean where does the web services sit in the Java EE EAR file hierarchy and how to invoke the deployed webs services?
It depends upon exactly how you implement your WebService and also on which Java EE version you are using. Simplest, with JAX-WS your webservice implementation and interface are all packed in the WAR. See the sun tutorial. Possibly you may implement your service as an EJB and in which case you can simply use the @WebService annotation. In which case you’re delivering the EJB jar.
Recommend you work through a few tutorials for the specific App Server you are using.