I'm going to suggest a few things.

1) Download a copy of Zen Cart to your local computer and unzip it there. There's a link to the download on the Zen Cart home page (link at top of screen). You'll be able to see the folder/file structure that way. You can also use the local copy to make your changes and FTP them to your site.

2) There's a ton of info in the Tutorials/FAQ and Wiki. Take a peek in there.

3) BE PATIENT! There's a learning curve with Zen Cart and lots of people find themselves and because they expect to get everything done at once.

4) Use the template/override system. You'll save yourself headaches later.