This reply may reflect the writer's seriously under-cafeinated condition, but, IMO, you'll likely do well by:

1. familiarizing yourself with just how subdomains work (cf: "virtual host").
   See http://httpd.apache.org/docs/2.0/vhosts/examples.html.
   and
   such terms as "mod_proxy" or "AliasMatch"
   and/or
2. clarifying your question;
   • ascertaining whether this is actually a Perl-related issue;
   • specifying the circumstances in which you expect (I gather) to call a script in root's cgi-bin from <edit> one or more</edit> subdomains.