At this moment, you must modified defaults.conf.tpl and domains.conf.tpl with 'customize rule'.
Change something like '# ScriptAlias /cgi-bin/ "/home/<?php echo $user; ?>/<?php echo $domainname; ?>/cgi-bin/"' to 'ScriptAlias /cgi-bin/ "/home/<?php echo $user; ?>/<?php echo $domainname; ?>/cgi-bin/"' and then run fixweb and restart-web.