You probably should consider reading the documentation for Tk::Pane. If you want a Pane to "stick" to the edges of a container, you need to specify the -sticky option.

What it sounds like you are trying to do based on your description: (strict clean and perltidy-ed)

use warnings;
use strict;
use Tk;
use Tk::Pane;

my $mw = new MainWindow;
$mw->geometry('500x500');
my $outerPane = $mw->Scrolled(
    'Pane',
    -scrollbars => 's',
    -sticky => 'nsew'
) ->pack( 
    -fill => 'both',
    -expand => 1
);
my $blueBar = $outerPane->Frame(
    -background => 'light blue',
    -height     => 40,
    -width      => 500
)->pack(
    -fill => 'x',
    -side => 'top'
);
my $innerPane = $outerPane->Scrolled(
    'Pane',
    -scrollbars => 'w',
    -sticky => 'nsew'
)->pack(
    -fill => 'both',
    -expand => 1
);
my $greenBar = $innerPane->Frame(
    -background => 'light green',
    -width      => 40,
    -height     => 500
)->pack(
    -fill => 'y',
    -side => 'left'
);

MainLoop;
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