Every time you call a script beginning /perl/ after the domain, Apache treats it as mod perl. So say you had this mapping:

Alias /perl/ /home/public_html/mod_perl/
<Location /perl>
   SetHandler perl-script
   PerlHandler Apache::Registry
   Options ExecCGI 
 </Location>
[download]

And let's also say that your web root dir is /home/public_html and that your have enabled script execution throughout your site, then calling the script as:

/perl/script.cgi
[download]

would invoke it under mod_perl, whilst calling it under the more appropriately named :) mod_perl, following existing directory mapping, ie:

/mod_perl/script.cgi
[download]

would not.

Bet you're totally confused now - sorry, it's very late...

.02

cLive ;-)

ps - to answer your question, only those in the 'perl' directory.