Actually, what I'd like to do is have a central Mojo CGI script and route URLs appropriately to Perl Controllers. So a single file receiving all the various web requests, let's name it mojo_router.pl for the sake of discussion. The routing would work as follows:

website.com/* - Legacy traffic
website.com/mojo/* - Anything in this subdirectory runs mojo_router.pl, which routes them accordingly

The problem I'm running into is that when running in CGI mode, the URL parameter Mojo detects is always /. For example /mojo/foo and /mojo/bar both get detected in CGI mode as /