How to import Hybrid android app as two different modules?

Hello,
    I'm a former Eclipse user in the process of migrating to IDEA.  I'm using Cordova to develop hybrid apps.  To put this simply, I have a directory and a subdirectory within it I would like to add as two seperate modules.  My goal is to have one module be where I do my web-based development and the other where I work with the Java parts.

My current understanding of IDEA is that if I just used the parent directory of my app, I wouldn't be able to do Java builds correctly as all the source files would be in a subdirectory within the module.  Also, the directory structure needs to remain intact so that my web-based framework (Sencha Touch) will be able to successfully perform builds.

  Any help would be appreciated!