As shown in the following image the input textarea of the Disqus is just plain. Is there a way so we can add wysiwyg (like CKeditor) to it? And that input textbox always located at the top of comments, Is there a way so we can shift it to the bottom of the comments (like core comment module of drupal 7)?
Unfortunately, this is impossible. The Disqus comment form is in an iframe originating from disqus.com. It is basically a separate web page embedded within the content of your website.
If your page were to access the Disqus form, it would violate the Same-origin policy. This policy is to keep your information safe. Imagine if another page could read or modify data when you log in to your bank. Bad news.