Recommended Java EE project structure

I'm new to IDEA, fairly new to Java EE and switching from NetBeans..

NetBeans will create separate directory structures for web and ejb modules as sub-directories of the main project -
project-name/
project-name/project-name-ejb
project-name/project-name-war
In IDEA a Java EE project set up using the wizard shows 2 application modules EJB and Web in application.xml but these do not have separate directory trees in the project view, i.e., they are not separate IDEA modules.

For a project that may potentially have more than one web and ejb module is it best to set up a blank project and then create the modules so each has it's own separate directory structure?
I'd appreciate some insight into the pros and cons of the differing approaches.

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