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Best Practices for Project Organization Question

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I could use a tip or two on how to organize my projects and the way objects
are referenced.

I created a two projects, a "Web Application" project and an EJB project. I
created "Enterprise Application" project and added the other two to it. Now
I can easily access items (including a singleton class) in the EJB project
from a servlet in the "Web Application" project, via an EJB reference.

In the EJB project, the wizards allowed me to create an XSD, a WSDL and a
new "Web Service from WSDL". However, on deployment, Glassfish warns me
that the new web server annotated class will be treated only as a POJO
because it is in a war and not a jar file. But I need a web service, open
to the outside.

Question - What the best way to create Netbeans projects such that I can
create a web service EJB that can easily access the EJB my servlet interacts
with? (Note that I realize that the EJBs themselves are not singleton and
have coded up the data elements accordingly - I think)

Thank you
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