was created to help you with problems like this so e.g. instead of your App::Main you'd have an invocation script like:
prefix => 'App',
default => 'one',
This should do what you want (including the path info dispatch), but CGI::Application::Dispatch has lots more configuration options should you need more power.
Having said this, I now prefer CGI::Prototype over CGI::App, beacuse with CGI::Prototype, run modes are handled by classes so each of your two dozen (and growing) run modes would live in its own small module. I find this makes the application a lot more manageable as it increases in size.