#!/usr/bin/perl
use strict;
use warnings;
use Tk;

my $mw = new MainWindow;
$mw->geometry("360x250+280+60");
$mw->bind('<Escape>' => sub { $mw->destroy });
$mw->configure(-title => 'Test Checkbox Alignment');

# Main frame
my $mf = $mw->Frame->pack( -side => 'bottom', -pady => 1 );

# Inner frames
my $frm_l = $mf->Frame->pack( -side => 'left',  -pady => 1 );
my $frm_r = $mf->Frame->pack( -side => 'right', -pady => 1 );

my $qv;
my $qv_cbox = $frm_l->Checkbutton(
   -text     => 'QuickCheck',
   -variable => \$qv,
)->pack(
   -anchor => 'w',
);

my $dg;
my $dg_cbox = $frm_l->Checkbutton(
   -text     => 'Systems Guide',
   -variable => \$dg,
)->pack(
   -anchor => 'w',
);

my $yb;
my $yb_cbox = $frm_l->Checkbutton(
   -text     => 'Study',
   -variable => \$yb,
)->pack(
   -anchor => 'w',
);

my $pv;
my $pv_cbox = $frm_l->Checkbutton(
   -text     => 'Analyze',
   -variable => \$pv,
)->pack(
   -anchor => 'w',
);

# Create 2nd set of check boxes.

my $rd;
my $rd_cbox = $frm_r->Checkbutton(
   -text     => 'Read',
   -variable => \$rd,
)->pack(
   -anchor => 'w',
);

my $oc;
my $oc_cbox = $frm_r->Checkbutton(
   -text     => 'Configure',
   -variable => \$oc,
)->pack(
   -anchor => 'w',
);

my $hr;
my $hr_cbox = $frm_r->Checkbutton(
   -text     => 'Troubleshoot',
   -variable => \$hr,
)->pack(
   -anchor => 'w',
);

my $tm;
my $tm_cbox = $frm_r->Checkbutton(
   -text     => 'Prioritize',
   -variable => \$tm,
)->pack(
   -anchor => 'w',
);

MainLoop;
[download]

Feel free to reorder the widgets how you need them to be.

Regards, Ştefan

P.S. It's also the way I would do the layout.