Calling external Libraries in WordPress

In your functions.php add this code

function load_custom_script() {

    wp_deregister_script('jquery');
    wp_register_script('jquery', 'https://ajax.googleapis.com/ajax/libs/jquery/1.6.2/jquery.min.js', false, '1.6.2');
    wp_enqueue_script('jquery');

    wp_register_script('jquery.flexslider', get_bloginfo('template_directory').'/jquery.flexslider-min.js', array('jquery'));
    wp_enqueue_script('jquery.flexslider');

}

function load_custom_style() {
    wp_register_style('flexslider', get_bloginfo('template_url').'/flexslider.css', array(), '');
    wp_enqueue_style('flexslider');
}

add_action('wp_print_scripts', 'load_custom_script');
add_action('wp_print_styles', 'load_custom_style');

Do not forget to remove your code

<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.6.2/jquery.min.js"></script>

<link rel="stylesheet" href="<?php echo get_bloginfo('template_directory'); ?>/flexslider.css" type="text/css" media="screen" />
<script src="<?php echo get_bloginfo('template_directory'); ?>/jquery.flexslider-min.js"></script>