[eluser]Michael;[/eluser]
Greetings...
Each subdomain is a folder in your webroot, i.e.:
public_html
->subdomain1
->subdomain2
So, all you have to do is make each subdomain it's own application.
What I have done with CI is sperate it out so that the system folder is outside the webroot, then each domain/subdomain is in it's own folder, like so:
system
public_ftp
public_html
->default //this is the main domain
->subdomain1
->subdomain2
index.php //this is the index that points to 'default'
subdomain1.php //points to subdomain1 application
subdomain2.php //points to subdomain2 application
With this setup you can easily segregate your member groups so that each have their own subdomain and CI application. Each subdomain will have it's own index.php so if you go to subdomain1.example.com you'll hit the subdomain1 folder and it will run as it's own application... or, if you are surfing the "main" default site you would be able to have link such as example.com/subdomain1.php/controller/method ... etc to lead them to the group application.
Hope this helps, good luck.