If your .ejb3 is a top level deployment it should work - see JARStructure.
If not, then you either need:
* META-INF directory
* add .ejb3 to JarUtils
Do you use an IDE as Eclipse (with WebToolsPlatform-Plugin or JBossTools)? If yes: they allow to export an Enterprise Application as EAR file. This is the easiest way to do so.
If you don't have an IDE, I would advice to start from scratch: get a book which explains the JavaEE5 concepts and the deployment structure, or find a basic tutorial in the internet.