Here is a walkthrough of a multimodule project I created with eclipse Kepler.
1) create mymodule1 as a normal dynamic web project
Set target runtime : Google App Engine (x.x.x)
Set Add project to an ear: selected
Set EAR project name: myear
This will create two eclipse projects, one associated with the module and the other with the ear file:
mymodule1
myear
In the appengine-application.xml of both these projects set
<application></application>
to both hold the name of your GAE project (e.g. mygaeproject-11111)
This name you should have already created in the cloud console, and will hold the multiple modules.
2) In the appengine-application.xml of mymodule1 under
<application>mygaeproject-11111</application>
add...
<module>mymodule1</module>
(Otherwise you end up with a "Multiple entries with same key" exception later)
3) In the appengine-application.xml of mymodule1, add the instance class you want the module to run on (inside appengine-web-app), for example:
<instance-class>F2</instance-class>
3) From the project menu clean both mymodule1 and myear. You can now deploy myear to your local google app server if you wish.
4) You will also need a default module to deploy to a production server, so Create mymodule2 as a normal dynamic web project
Set target runtime : Google App Engine (x.x.x)
Set Add project to an ear: selected
Set EAR project name: myear
5) In the appengine-application.xml of mymodule2 set the following, and set an instance class like before.
<application>mygaeproject-11111</application>
<module>default</module>
6) In the application.xml (Not appengine-application.xml) of myear set the context root associated with
<web-uri>mymodule2.war</web-uri>
to
<context-root>default</context-root>
7) Ok now clean and build everything again and deploy to your local google app server.
If all looks good simply rightclick on the server in the servers panel and select... Deploy to remote sever
8) If later you want to kill the project select it in your cloud console, then go to settings in the left pane and click disable application.