I just ran the layout according to your folder structure on Linux system.
I added a standard htaccess file, as you will find in the codeigniter user guide. So there are two .htaccess files. One in the main folder of the application (root), and the other in the administration folder.
Removed index.php from $ config ['index_file'] = '' in both configuration files.
A Home controller was created in both cases using the whoami method, which simply returns the echo "I am the administrator control home page" for the administrator. The home controller called / Administration / home / whoami and "I am the main home controller" for / home / Whoami.
Both returned corresponding messages indicating that each of them was correctly called.
.htaccess directly from the user guide.
RewriteEngine On RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d RewriteRule ^(.*)$ index.php/$1 [L]
So, I think the same should work with IIS, but don't keep me that way. I found something that might help there ... version of .htaccess .
So, for the above setup, you must be able to host the appropriate URLs to get into both CI instances.
source share