im not very familiar with cutenews, but what you would have to do is go into the cutenews files (mainly the ones which link to the comments pages) and modify the comments links which are probably formatted something like comments.php?id=$article_id . youd have to change it to something like say ?id=article_comments&art_id=$article_id then just make sure your index.php looks for the article_comments variable so that if it is called, have it include the cutenews comments file in your usual content area in the form of comments.php?id={art_id variable}
keep in mind, not all of this (very little of it ;) ) is the actual code. you will need to do some self investigating and change what needs to be changed. but the structure should be correct.