For Phonegap/Cordova development, today, the end-user is expected to manually create a new Android Application Project via their Eclipse plug-in. Then the end-user is instructed to tweak the AndroidManifest.xml and MainActivity.java, plus place Cordova.js and Cordova.jar in the correct locations. All of these steps could be automated.
A decent doc on the end-to-end process
http://www.adobe.com/devnet/html5/articles/getting-started-with-phonegap-in-eclipse-for-android.html

In both the XCode/iOS and well as the Eclipse/Android project variations, the HTML+JS+CSS go inside of a www directory - this directory can be the same structure as our normal HTML5 archetype-generated "webapp" directory.