Hi,
When i build a website, I keep all my php/html files in a folder 'files', all images in the 'images folder', so do for css and admin. I keep only one index.html file in my root folder. I've put a javascript redirect in the index file.
So whenever you type in www.sufixe.com, it will be redirected to www.sufixe.com/files/index.php

Is this going to affect my results in google?

only insofar as the googlebot can't crawl your site at all. other than that it should be just fine.