If I understand it right, you have multi-directory application with many scripts in them. If that is so, then every directory that your CGI application have will become Mojolicious::Controller, every script will become URL, and all logic will go to appropriate Controller.

If you have something like this in your application directory:

.. 
index.pl
dir1/somescript1
dir1/somescript2
dir2/somescript3
dir3/somescript4
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then your Mojolicious application will have something like this inside:

script/app.pl
lib/App.pm
lib/App/Controller/Main.pm
lib/App/Controller/Dir1.pm
lib/App/Controller/Dir2.pm
templates/layouts/default.html.ep
templates/main/index.html.ep
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script/app.pl:

#!perl

use strict;
use warnings;
use FindBin;
BEGIN { unshift @INC, "$FindBin::Bin/../lib" }
use Mojolicious::Commands;
Mojolicious::Commands->start_app('App');
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lib/App.pm:

package App;
use Mojo::Base 'Mojolicious';

sub startup {
   my $self = shift;
   my $r = $self->routes;
   $r->get('/')->to('main#index');
   $r->get('/dir1/somescript1')->to('dir1#somescript1');
   $r->get('/dir1/somescript2')->to('dir1#somescript2');
   $r->get('/dir2/somescript3')->to('dir2#somescript3');
   $r->get('/dir2/somescript4')->to('dir2#somescript4');
}
1;
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lib/App/Controller/Main.pm:

package App::Controller::Main;
use Mojo::Base 'Mojolicious::Controller';

sub index {
  my $self = shift;
  # will render templates/main/index.html.ep
  # logic from index.pl  
  $self->render();
}
1;
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lib/App/Controller/Dir1.pm:

package App::Controller::Dir1;
use Mojo::Base 'Mojolicious::Controller';

sub somescript1 {
  my $self = shift;
  my $params = $self->req->params->to_hash;
  # logic from dir1/somescript1.pl
  # all HTML goes to templates/dir1/somescript1.html.ep
  $self->render();
}
# etc...
1;
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Then you run it from root of your application like this:

perl script/app.pl
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update: I thought that you might want to read the docs: Mojolicious Tutorial, Growing Guide