With Eclipse, it's better to create multiple projects and assemble them in a EAR project. Doing this makes better separation and dependency management.
EJB module (EJB -> EJB Project)
attach Java doc: expand server library (Jboss) and attach javadoc (http://docs.oracle.com/javaee/6/api/)
Vaadin UI web project
NOT select "generate web.xml"
select "create project template" and customize package name
Note: on step-by-step reference it's instructed not to select project template. however, doing this ivy.xml is not created and vaadin library becomes missing
Portlet version: no portlet
add vaadin CDI library (see below, setup CDI)
common utility project module (Jave EE -> Utility Project)
Enterprise Application EAR project (Jave EE -> Enterprise Application Project)
create last
select previously created projects in "Jave EE module dependencies"
"Generate application.xml deployment descriptor" : not necessary but may be helpful
the main project for server deployment
manages the other projects
deploy only the EAR project to server
all modules are deployed within the EAR