[eluser]Michael Wales[/eluser]
CI is a framework that runs on your webhost. So, while developing your site (in WAMP) everything will be in your htdocs folder, just as if you had developed all of the files yourself.
Then, when it's time to go live - simply upload to your hosting.
The framework is nothing more than a collection of php files. There's no IDE, scripts, etc, that you will have to pull out prior to going live.