removing index.php (docs are kinda sucky for this)

[eluser]xwero[/eluser]
.htacces files are cascading. If you put the file in your root directory all subdirectories will have the same redirecting rules. if you put it in a sub directory with other redirection rules those rules are only valid for that subdirectory and all its subdirectories.

Here you can find a good introduction to .htaccess . It's not really in the reach of CI to explain mod_rewrite because there are other webservers than apache and they can have other ways of rewriting urls.