[themes] Autogenerated Lists

Hi.

I am Miles Rout, and I'm currently converting a static HTML theme to a drupal theme. I've been wondering about the use of:

<?php print theme('links', $primary_links, array('class' => 'links primary-links')) ?> and <?php print theme('links', $secondary_links, array('class' => 'links secondary-links')) ?>

When I use these, should I need to change my CSS? Do they output the list in a funny way? Why is this using a theme(); function when they could just be <?php print $primary_links ?> or something like that? Or alternatively, why isn't the page_title something like <?php print theme('title', $page_title, array('class' => 'title page-title')) ?> ?

Thanks, Miles