but even though the new window comes up fine the original subroutines does not wait for an answer from the new window

That's the normal behaviour for a window. If you don't want that, you should create a dialog instead.

Armed with that knowledge, you should be able to find the documentation and examples yourself.

#!/usr/bin/perl -w
use strict;
use warnings;

use Tk;

my $mw = MainWindow->new();
$mw->withdraw();

my $ftp_warn = $mw->messageBox(
  -title   => 'Silly message',
  -message => "We are displaying a silly message, do you wish to conti
+nue?",
  -type    => 'YesNo',
  -icon    => 'question',
);

if ( $ftp_warn eq 'No' ) {
  exit;

  }else {
    my $msg2 = $mw->messageBox(
    -title   => 'Really?',
    -message => "We displayed silly message and you wish to continue?"
+,
    -type    => 'OK',
    -icon    => 'question',
  );

while (1){
print "hit control-c to exit\n";
sleep 1;
}

}
[download]

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

#set up main window display
use Tk;
my $mw = new MainWindow(-title => 'PopUp');
my @buttons = qw(A B C D E F G);

#popup menu set up
my $popupmenu = $mw->Menu(-tearoff => 0);

    foreach my $bt (reverse @buttons){
            $popupmenu->insert(0, 'command',
               -label => $bt,
               #-command => [sub {print $popupmenu->cget('text') ."\n"
+}],
               -command => [sub {print $bt ."\n"}],
          );
    }


$mw->bind("<Button-3>" => sub {$popupmenu->Popup(-popover => "cursor",
                                    -popanchor => 'nw'),
                                -command => [sub {print "Popup\n"}]});


MainLoop();
[download]

Take a look at Common Dialogs in the widget demo for examples of what's available (with sample code via the See Code button).