wp_enqueue_script
function custom_theme_script(){
wp_register_style('bootstrap', get_stylesheet_directory_uri() . '/css/bootstrap.css' );
wp_enqueue_style('bootstrap');
wp_register_style('style', get_stylesheet_directory_uri() . '/css/style.css');
wp_enqueue_style('style');
wp_register_script('bootstrap', get_template_directory_uri() . '/js/bootstrap.min.js', array('jquery'), '20120206', true );
wp_enqueue_script('bootstrap.min');
}
add_action('wp_enqueue_scripts', 'custom_theme_script');