OK I am just a beginner with the package also but I did get it running with the html interface.
First copy the files to a directory your local webserver can access ( I used both iis & apache on my local development machine ) ie off the webroot directory.
Then run the new-phpdoc.php file using your web browser at address localhost://thedirectoryyouputthefilesin/new-phpdoc.php
That's what worked for me.
Hope that helps