Upon logging into your account, you are restricted to only your account and cannot move outside of it. When you log in, you are in what is known as the "root" of your account. In here there are several miscellaneous files and directories, all of which are important but none of which should be altered, removed or renamed. In short, do nothing with these files unless you are very sure you know what they do.
The only files and directories that you should care about are the "public_html" directory and below. The "public_html" or "www" (which are in effect the same directory) is where all of your files pertaining to your website should reside. Uploading files into the "root" of your account will mean that no one will be able to access them via the web.
The "public_html/cgi-bin" (main site cgi) directory is where all of your files pertaining to any cgi scripts (such as perl) should reside. When calling a script from there, as with all file, you must include the full public path: /cgi-bin/file.cgi'
The "public_ftp" directory is where all of your files pertaining to Anonymous FTP are located. Any files in your ftp directory will be available via Anonymous FTP if enabled. This function is disabled by default on all accounts since it has the potential to be abused.