[eluser]xadio[/eluser]
I would recommend copying your application directories and placing each one in the subdomain root. Then copy the index.php and modify each one. Since the index is now in the root of your application you will need to specify the system as '../system'. The application will be the current directory (or './application' depending on where you put the application).
I hope this makes sense if not check out this tree I've defined:
Code:
/
/system <-- CI System
/application <-- Main CI Application
/subdomain1 <-- Subdomain 1
/application <-- S1 CI Application
/index.php <-- S1 CI Index.php
/subdomain2 <-- Subdomain 2
/application <-- S2 CI Application
/index.php <-- S2 CI Index.php
... etc
