The skeleton directory is a basic layout that WHM uses for all accounts that you create under your reseller account. If you look inside the skeleton directory, you'll see that it looks very much like your own account when you log in and look around with your FTP client. That's no accident, since this file is the basis upon which all of your new accounts will be created.
You can alter the makeup of new accounts, as you see fit, by adding things to the skeleton directory. For instance, placing your own branded index.html file in the public_html directory inside the skeleton directory, will result in a branded index page on every account that you create.