For numbering, in your comment.php, change this:
wp_list_comments('callback=mytheme_comment');
To this:
wp_list_comments(array(
'callback'=>'mytheme_comment',
'style'=>'ol',
));
For separation into comments and pingbacks, you’d do something like this:
wp_list_comments(array(
'callback'=>'mytheme_comment',
'style'=>'ol',
'type'=>'comment',
));
wp_list_comments(array(
'callback'=>'mytheme_comment',
'style'=>'ol',
'type'=>'pings',
));