If you follow the instructions here, this will create a modularized application structure in Eclipse, and not using Maven at all. You will need Eclipse WTP in order to have the required project types available (Enterprise Application Project and Dynamic Web Project).
The Eclipse project structure should look as follows:
<<Enterprise Application Project>> ear-app
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| (refers to)
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<<Dynamic Web Project>> app-module-1 "default"
<<Dynamic Web Project>> app-module-2 "any_name_2"
<<Dynamic Web Project>> app-module-3 "any_name_3"
<<Dynamic Web Project>> app-module-4 "any_name_4"
The value of "name" refers to the "module" element in appengine-web.xml, while the physical web project can have any name.
Please note that you need to switch into J2EE perspective in order to have the GPE WTP menu options available, they do not show up in the standard Java perspective.
Next, you need to link the EAR project to a new local server instance (of type "Google App Engine").
Only one of the web modules must be flagged as "default" in appengine-web.xml.
Upon deployment of the EAR to the local server, the datastore location is in WEB-INF/appengine-generated/local_db.bin of the default web module, and it is shared between the web modules.