authentication code in index file created 404 error

I tried to authenticate my site by adding code to the ‘index file’ and when that failed I tried by adding code to the ‘header”. Now I receive a 404 error for my homepage but the rest of the site appears fine.
Will uploading a new index file fix this problem? What is the best way to authenticate this site without ruining it? Where and how do I get and upload an index file.