Adding CodeIgniter to an existing site

[eluser]Unknown[/eluser]
Hi everyone, Happy New Year.

I already have a site setup with folders structured in a certain way e.g.

mainsite
mainsite/css
mainsite/includes
mainsite/scripts
mainsite/media
mainsite/subsite1 (layout)
mainsite/subsite1content
mainsite/subsite2 (layout)
mainsite/subsite2content
etc etc

If I want to use codeigniter does it mean everything must now be restructured according to the folders for the codeigniter setup? Or can I keep my existing folder structure?

Thanks in advance.