if for example you want the news box to be unique find this bit
Code:
{ include file="menu.tpl" dingbats="dingbats_news.gif" menu_title=$lng.lbl_news menu_content=$smarty.capture.menu }
and change menu.tpl to the menu2.tpl
then make a copy of menu.tpl call it menu2.tpl and edit to suit your needs