Use different frames to separate widgets in columns when you are using pack, or use other geometry managers like grid, frame or place. A good source of inspiration is the widget demo script that comes with TK (enter 'widget' in the console).

The anchor option is for alignment.

use 5.010;                      # for say
use strict;
use warnings;
use Tk;

my $main  = MainWindow->new();
my $label = $main->Label( -text => "Presence Check" )->pack();

my $opt_ft  = [qw/-side top -expand 1 -fill both/];
my $opt_flr = [qw/-side left -expand 1 -fill both/];
my $opt_fb  = [qw/-side bottom -expand 1 -fill both/];
my $opt_c   = [qw/-side top -pady 2 -anchor w/];

my $fr_top   = $main->Frame()->pack(@$opt_ft);
my $fr_top_l = $fr_top->Frame()->pack(@$opt_flr);
my $fr_top_r = $fr_top->Frame()->pack(@$opt_flr);
my $fr_bot   = $main->Frame()->pack(@$opt_fb);

my ( $vbutton1, $vbutton2, $vbutton3 ) = ( 'OFF', 'ON', 'OFF' );
my $b1 = [
    [ 'button1', 'button 1', \$vbutton1, 'OFF', 'ON' ],
    [ 'button2', 'button 2', \$vbutton2, 'OFF', 'ON' ],
    [ 'button3', 'button 3', \$vbutton3, 'OFF', 'ON' ],
];

foreach my $btn (@$b1) {
    $fr_top_l->Checkbutton(
        -text     => $btn->[1],
        -variable => \$btn->[2],
        -offvalue => $btn->[3],
        -onvalue  => $btn->[4],
    )->pack(@$opt_c);
}

my ( $vbutton4, $vbutton5 ) = ( 'ON', 'OFF' );
my $b2 = [
    [ 'button4', 'button 4', \$vbutton4, 'OFF', 'ON' ],
    [ 'button5', 'button 5', \$vbutton5, 'OFF', 'ON' ],
];

foreach my $btn (@$b2) {
    $fr_top_r->Checkbutton(
        -text     => $btn->[1],
        -variable => \$btn->[2],
        -offvalue => $btn->[3],
        -onvalue  => $btn->[4],
    )->pack(@$opt_c);
}

my $button = $fr_bot->Button(
    -text    => "Exit",
    -command => \&exit_button
)->pack(@$opt_ft);

MainLoop();

sub exit_button {
    foreach my $btn (@$b1) {
        say "- $btn->[0]: $btn->[1] -> ${$btn->[2]}";
    }
    foreach my $btn (@$b2) {
        say "- $btn->[0]: $btn->[1] -> ${$btn->[2]}";
    }
    $main->destroy;
}
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Regards, Stefan.