To get AWStats to work at example.com/awstats/ rather than example.com/awstats/awstats.pl I replaced:
ScriptAlias /awstats /home/efy/cgi-bin
Alias /awstats /home/efy/cgi-bin <Location /awstats> Options +ExecCGI AddHandler cgi-script .pl DirectoryIndex awstats.pl </Location>
I have also found it useful to add
to the .htaccess file in Webalizer stats folders. This is in case I am overriding DirectoryIndex in ~/public_html.
Can anyone point me to the right place to get changes applied to all new virtual servers?