You need to do self joins. You can have one comments table but there can be parent_id for each comment.
http://stackoverflow.com/questions/3362038/what-is-self-join... this might help.
http://stackoverflow.com/questions/3362038/what-is-self-join... this might help.
Using hierarchy and recursivity like this: http://stackoverflow.com/questions/4216875/php-reorder-array...
see if that helps