You can read my article about how we did this for one application. In general, read some stuff about MVC (model-view-controller) for the web, look at some of the frameworks out there, and see what you like.

By the way, there is no need to invent something that maps URLs to Perl modules. Apache already handles every conceivable mapping through httpd.conf, and if you run mod_perl you can use things like Apache::Dispatch to simplify it even more.