When the downloaded archives are expanded, they will automatically expand into the desired structure. You must retain that structure when transferring files between computers. For your reference, Appendix II contains a detailed list of all files and folders, describing what they do and where they belong. It does not use absolute paths at all, however. In this step, you customize the CGI script files.
Different systems have different rules about which extension to use.
Others allow only .cgi, and others allow only .pl. Still others require .plx or other weird names. Ask your administrators, or copy the extensions of working scripts, or experiment to find the extension that works for you. When you open the script file to edit the path to Perl, use the most hardcore text editor you have. Like, Notepad on Windows, Simple Text on Mac, vi on Unix.