CI's default folder structure is really geared towards one site domain, and having both the application folder and the system folder visible to the browser is not exactly a secure approach. By configuring your install to support multiple sites, not only do you make the updating of the CI core easier, but also make the CI install more secure as a whole.
The example is on a Windows system, but the instructions are generic enough to work on any platform. They're using it under a XAMPP install, but the changes are all below the document root of that setup. You'll need to edit some of the config files and be able to update the Apache configuration to work with VirtualHosts