package My::App;

use strict;
use warnings;
use base qw(CGI::Application BLL::OtherPackage);

sub setup {
    my $self = shift;

    $self->mode_param('section');
    $self->start_mode('home');
    $self->run_modes(
        'here_sub'   =>    'here_sub',
        'test_rm'    =>    'sub_in_other_file',
    );
}

sub here_sub {
    my $self = shift;
    # no problems using self here
}

1;

### Separate file
package BLL::OtherPackage;

use strict;
use warnings;

sub sub_in_other_file {
   my $self = shift;
   # $self would be what I expected if I didn't put this in 
   # the 'use base' or @ISA for that matter. What an abuse.
}
1;