Just some basic questions about structure

[eluser]egbertwietses[/eluser]
Let's say you have a clean CI install with a structure like this:
public/
/css
/js
/etc
system/
/all ci related stuff

Now I want to create a site with cms
I want to share my models for the cms and the site.
Let's say I want to use the following url structure

www.example.com = site
www.example.com/cms = cms

Now if I follow the default set up everything for the cms ends up in one controller.
Should I solve this with routing or use a modular setup?