I normally do the following for APPLICATIONS or PROGRAMS that need a members area and a admin area:
domain/index.php(or html)
domain/styles/images/<images>
domain/styles/stylesheet.css
domain/includes/functionlists.php
domain/classes/stuff.php
domain/mem/index.php
domain/acp/index.php
Depending on what you do I change it up, there are a lot of ways you can do it...
You just need to remember that folders are helpful. When you create a set of pages that are all linked to one another and they have a specific purpose, like showing the user a bunch of images or something, you should put into a directory like
www.domain.com/portfolio/page.php instead of placing all the pages into the main directory.
Just do it how you'd do it on your own computer, you want large quantities of files to be seperated and organized, if you only have a few files you may not have any folders. (maybe /images or /styles)