Handing Multiple Sites

[eluser]Insa[/eluser]
I'm trying to run multiple applications with CI, a site and an admin section for said site.

I have 2 application folders: 'application/site' and 'application/admin', and I would like them to be accessed on site.com and site.com/admin.

the article in the user guide about this helped me get the 'site' part working properly, but it wasn't clear on what to do for the 'admin' app.

The problem I'm having is that I'm unsure where to put the index.php file for admin. I can't make a directory 'admin' and place the index file in there, because if I go to site.com/admin, CI will look at 'site/controllers/admin.php' instead of where I want it to look.
I also tried renaming index.php to admin.php and putting it 'site/controller's, but all I got was error messages because it tried to define statics etc etc twice.

How do you guys handle this problem? I've been struggling with it for the past few hours, and as I can't figure it out myself I figured I'd give these forums a try.

Thanks in advance!