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;
[download]

Ahhhh. Yes, I definitely should read that. I'm indebted to you my friend!

(probably simple) ... and no sign of the inside pane or green bar. Please shed some wisdom on me, where are my widgets?!

:) it never is

When trying to figure stuff like this out, add -bg to every widget

Also add a label or other widgets like Re: TK Gui Help

See Tk::pack for description of the algorithm

Use Tk::WidgetDump to see what p> See sub Tk::Widget::Scrolled and sub Tk::Frame::AddScrollbars actually does

#!/usr/bin/perl
use strict;
use Tk;
use Tk::Pane;

my %frames;  
my %subframes;
my %labels;
my %buttons;
my $mw = MainWindow->new;

my $pane = $mw->Scrolled("Pane",
   -scrollbars => 'se',
   -sticky => 'nsew',
   -bg => 'black',
   -width => 300,
   -height => 300
)->pack(-expand => 1, -fill => 'both');
my $realpane = $pane->Subwidget('scrolled');

my $xbar = $pane->Subwidget('xscrollbar');
my $ybar = $pane->Subwidget('yscrollbar');

$ybar->configure(-background=>'blue', -activebackground=>'blue', 
                  -troughcolor => 'black', -width=> 50);
$xbar->configure(-background=>'green', -activebackground=>'green',
                 -troughcolor => 'black', -width=> 50);


foreach my $row (0 .. 3) {
    $frames{$row} = $pane->Frame(-bg => 'black')->pack(
     -padx => 5,
     -pady => 5,
     -expand => 1,
     -fill => 'both', 
     -anchor => 'nw',
   );
  
   foreach my $col (0 .. 3) {
      createTile($row, $col);
   }
}

MainLoop;

sub createTile
{
   my ($row, $col) = @_;

   $subframes{$row}{$col}{'mainframe'} = $frames{$row}->Frame(
        -bg => 'black')->pack(
                           -side => 'left',
                       -padx => 5,
                           -pady => 5,
                           -expand => 1,
                           -fill => 'both', 
                           -anchor => 'nw',
        );

   my $frame = $subframes{$row}{$col}{'mainframe'};

   my $sc = $frame->Scrolled('Canvas',
      -scrollbars => 'osoe',
      -scrollregion => [0, 0, 1200, 1200],
      -width => 125,
      -height => 125,
      -background => randColor()
   )->pack(-fill=>'both',-expand => 1, -side =>'top');

   my $count = int(rand(6)) + 2;
   foreach my $i (1 .. $count) {
      my ($x, $y) = (randNumber(), randNumber());
      my $size = randNumber();
      $sc->createRectangle($x, $y, $x+$size, $y+$size,
         -fill => randColor(),
         -outline => 'black',
         -width => 2
      );
   }

   #miniframe for labels
   $subframes{$row}{$col}{'subframe_a'} = $frame->Frame(
           -bg => 'black')->pack(-side => 'top',-expand=> 1,-fill=>'bo
+th');
   #mini frame for buttons
   $subframes{$row}{$col}{'subframe_b'} = $frame->Frame(
           -bg => 'black')->pack(-side => 'top',-expand=> 1,-fill=>'bo
+th');

   #labels
   $labels{$row}{$col}{1} = $subframes{$row}{$col}{'subframe_a'}->Labe
+l(
        -text => "$row - $col" ,
        -bg => 'black',
        -fg => 'green',
     )->pack(-side => 'left', -padx => 5);

  $labels{$row}{$col}{2} = $subframes{$row}{$col}{'subframe_a'}->Label
+(
        -text => "$row - $col" ,
        -bg => 'black',
    -fg => 'hotpink',
     )->pack(-side => 'right', -padx => 5);

   #buttons       
  $buttons{$row}{$col}{1} = $subframes{$row}{$col}{'subframe_b'}->Butt
+on(
       -text => " Zoom Out ",
       -command => sub { $sc->scale(qw/all 0 0 .5 .5/); }
   )->pack(-side => 'left', -padx => 5);

  $buttons{$row}{$col}{2} = $subframes{$row}{$col}{'subframe_b'}->Butt
+on(
       -text => " Zoom In",
       -command => sub { $sc->scale(qw/all 0 0 2 2/); }
   )->pack(-side => 'right', -padx => 5);
}

sub randColor {
   my @colors = qw(red yellow blue orange green purple);
   return $colors[rand($#colors + 1)];
}

sub randNumber {
   my ($max, $min) = (100, 10);
   my $size = int(rand($max));
   $size += $min if $size < $min;
   return $size;
}
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