How do you plan your CI applications?

[eluser]Colin Williams[/eluser]

how do you arrive at figuring out those controllers?

Typically there is one controller per resource. Let's say we're making a CMS. Depending on how you design it, let's say your resources are Pages, Users, and Categories. This lends to a Page controller, User controller, and Category controller. That's a very basic example but I hope it explains the idea. Models typically follow suit but are more burdened with the complexities of these resources.