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;