Flexible intranet development. Taking thoughts.

[eluser]vasocreta[/eluser]
Hi, CI coders!

I am 3 days old to CI, coming from a Fusebox (intermediate) background. Fusebox presented some issues for me as I tried to think through a current project where I am developing an intranet for my workplace. I work in education and the challenge that faces me is that my itty-bitty organization at the university requires an intranet that will be made up of many micro-sites. There are about 10-15 different working groups and each group is in charge of their own content. As it turns out, each group wants to incorporate their own designs for their little section of the intranet as well.

In this case, I feel that Fusebox allowed me a bit more of a straightforward path to achieving this. But I want to use CI.

So...onto the question, eh?
When setting up controllers, I was thinking that each controller would represent a group. Is this the best way to think about this? I guess I am so used to using hierarchy of folders (Circuits, for you Fusebox speakers) to structure my backend. With CI, it seems that each controller is simply a file rather than a folder that contains files.
Can the controller folder contain folders? Is there a reason to even do that?

That is enough from the noob for now. I appreciate any insight I can gain from all of you. I have heard about the CI community and that is a big part of what made me want to try this framework.