Directory access newbie question

[eluser]Kurai[/eluser]
I've installed codeigniter, and, for some reasons, I had to use some directory which are external to the CI engine. I've noticed these directories show the file list if directly accessed. So I just copied the index.html file with the forbidden message to all my directory. I haven't access to httpd.config, so, I guess it's the easiest way to do this. Or is better to do it via .htaccess?

Another question: I've noticed that system directory is accessible as well, and that the guide tells to use a not-so-obvious name to avoid direct access. Now, I'm confused. I tried to put the index.html there, and everything seems to work fine (note: I'm not using a database). Is it possible to have problem ith this solution? And if not, why not to include a index.html in the system directory? I'm a bit confused.

Thank you!