It was difficult to understand what you were asking.
If you need to share resources between multiple applications, it's usually best to configure one directory to hold those resources, then configure each application to point to that directory. If you need application-specific resources, it's easiest to just add a directory named after the application inside the shared directory, but you could take the extra step of setting up individual directories along with the shared directory.
In most cases, I would setup my application something like this:
/public - index.php, assets directory containing all public files, including images, JS, CSS, and documents
/system - CI/system directory
/application - application directory
/application2
/application3
/application{etc.}
Of course, since index.php usually needs to be configured for each application, you may need several versions of this file, possibly in different locations, but you can still point to a shared location for the shared resources. You could even put application directories in your public directory to hold your index.php files and application-specific resources.
If I need shared non-public resources, I can add another directory for those and add it to the package paths in my applications or add a custom loader to load resources from multiple directories. Since I usually use Bonfire, I could place the shared code in my /bonfire directory, since Bonfire's loader is already setup to check the application, bonfire, and CI directories.
