It is good practice to modify files in the root of the project, and not in the platform folders.
The idea is to have common code for all platforms.
To have html / js for the platform, you can use a folder merges, and you can also use hooks for special settings.
, - ( cordova 3.3), , , , AndroidManifest.xml, .
www- , , cordova build cordova prepare www ( cordova plugin add ).