The first thing you will need to do is add a text field to your orders_Update.php page.
The second thing is to add it to the email, which you could do with Universal Email or update it manually by updating the shipping_confirm.php page which is located under the WA_Universal_Email folder/Email_Templates folder. and the code you will need to add could be something like this:
<?php if(isset($_POST['customernote'])) { ?>
<p>Note to Customer:</p>
<p><?php echo $_POST['customernote']; } ?>
</p>
assuming you text field is called customernote.