How to set Fancy Comments to appear below WordPress comments?

The link you have posted is redirecting to a bbPress forum topic. You can place the following code in the functions.php file of your active theme to place the Facebook Comments form after the bbPress reply form.

function heateor_ffc() {
    echo do_shortcode( '[Fancy_Facebook_Comments]' );
}
add_action( 'bbp_theme_after_reply_form', 'heateor_ffc' );

You can check other actions in the template file at the link and replace bbp_theme_after_reply_form with the desired action in the code posted above, if you want to change the position of the Facebook Comments form.