The reason why it didn't work was because I hadn't loaded the url helper class... DUH! Stick this in the constructor of your controller or autoload it in your autoload.php configuration file.
$this->load->helper('url');
Now you can use the base_url() function to get the url path from where to look for those files, e.g.:
<link rel="stylesheet" href="<?php echo base_url(); ?>styles/main.css" type="text/css">
This will load a css file called main.css from a folder called styles which is just under the base url folder codeigniter. On my PC it will find the file from: C:\wamp\www\codeigniter\styles\main.css
I reckon the creators of CodeIgniter should have added a constant through which to refer to the base_url and similar paths, or at least make the url class have static functions so url::base_url() can be called instead of base_url() which could be confused for a normal PHP function.
