If John's mythology has the root of the site down one level (say /dnn) and makes the URLs look like they are at then top level without any nasty GoDaddy redirection, which screws up Google and friends, then it is the right way to go.  By being down one level the directory permissions can all be correct simply by setting the correct permission on /dnn (before installing the files and subdirectories).  I plan on trying John's mythology soon on  a second site for testing.  Be advised that GoDaddy can (and has for me) messed up the protections on my directories. It was easier to FTP the site to my localhost, delete the files at GoDaddy, recreate and set the permissions on the top level directories and FTP the files back. Using GD's tools set set the permissions on 100s of subdirectories is no fun.

/DaveS

Thanks GreenFlash.  Feedback like that is always appreciated and "fuels the community spirit".