To use WordPress' version of jQuery that comes bundled with it, you need to enqueue it just like the other libraries. In functions.php:

add_action( 'wp_enqueue_script', wp_enqueue_script( 'jquery' ) );

Usage

In your HTML file, you can add the script tags just before the closing body tags like so:

<script>
  (function($) {
    console.log('Yay!');
  })(jQuery);
</script>

</body>
</html>