Custom post type category permalinks and archive pages

Yev, without a code sample to work from I’m not sure how helpful I can be but I’ll give you the code that I use for creating Custom Post Types with a archive page. This example will get you started for an FAQ (easily modified).

Note the rewrite lines and the flush, which is what creates a permalink structure for the Custom Post Types (and flushes the cache to activate it). I suspect this will get you fairly close to what you’re hoping for but if not, submit your code and I’ll try to help.

if ( ! function_exists( 'new_cpt_faq' ) ) {
    function new_cpt_faq() {
        register_post_type( 'new_cpt_faq',
            array(
                'labels' => array(
                    'name' => __( 'FAQs', 'name_space'  ),
                    'singular_name' => __( 'FAQ', 'name_space'  ),
                    'add_new' => __( 'Add New FAQ', 'name_space'  ),
                    'add_new_item' => __( 'Add New FAQ', 'name_space'  ),
                    'edit_item' => __( 'Edit FAQ', 'name_space'  ),
                    'new_item' => __( 'New FAQ', 'name_space'  ),
                    'all_items' => __( 'All FAQs', 'name_space'  ),
                    'view_item' => __( 'View FAQ', 'name_space'  ),
                    'search_items' => __( 'Search FAQs', 'name_space'  ),
                    'not_found' =>  __( 'No FAQs found', 'name_space'  ),
                    'not_found_in_trash' => __( 'No FAQs found in Trash', 'name_space'  ),
                    'parent_item_colon' => '',
                    'menu_name' => __( 'FAQs', 'name_space'  )
                ),
            'public' => true,
            'has_archive' => true,
            'supports' => array( 'title', 'editor' ),
            'rewrite' => array(
                            'slug'=>'faqs',
                            'with_front'=> false,
                            'feed'=> true,
                            'pages'=> true
                        )
            )
        );

        flush_rewrite_rules();
    }
}
add_action( 'init', 'new_cpt_faq' );

if ( ! function_exists( 'new_cpt_faq_taxonomy_categories' ) ) {
    function new_cpt_faq_taxonomy_categories() {
        register_taxonomy(
        'new_cpt_faq',
        'new_cpt_faq',
        array(
            'labels' => array(
            'name' => __( 'FAQ Category', 'name_space'  ),
            'add_new_item' => __( 'Add New FAQ Category', 'name_space'  ),
            'new_item_name' => __( 'New FAQ Category', 'name_space' )
            ),
            'show_ui' => true,
            'show_tagcloud' => true,
            'hierarchical' => true
        )
        );
    }
}
add_action( 'init', 'new_cpt_faq_taxonomy_categories' );

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