How to setup a permalink structure for a custom post type

I think you need to use the rewrite argument.

Here’s an example setting the url to tips

$args = array(
    'public' => true,
    'publicly_queryable' => true,
    'show_ui' => true, 
    'show_in_menu' => true, 
    'query_var' => true,
    'rewrite' => array( 'slug' => 'tips' ), // Here!
    'capability_type' => 'post',
    'has_archive' => true, 
    'hierarchical' => false,
    'menu_position' => 20,
    'supports' => array( 'title', 'editor', 'author', 'thumbnail', 'excerpt', 'comments', 'revisions', 'custom-fields')
  ); 

  register_post_type( 'tips', $args );

More info: http://codex.wordpress.org/Function_Reference/register_post_type