I changed my themes index.php and now my categories don’t list!!

I recently changed my wordpress theme’s index.php to not list any of my defalut latest blogs and instead, have links to all my most commented posts.

The problem is this…

In my actual posts page, when the readers click the category the post is from, it takes them to that categories permalink but it’s listing my index.php’s content again. Also, when I use the search box… it does the same thing.

Before I revamped the index.php, it listed my most recent posts with paging and i guess it would filter that page to fit the category pull… but now it’s just listing my front page.

I’m assuming I have to create a new file for my blog listings and point my blog address there but I don’t know how to create a new page in my template for my blog to recognize.

What do I do?