pack and place are for positioning subwindows inside a window, they should not matter.

Lacking code from you, here's a small example that puts up a main window and a top level window exactly where they are supposed to be.

#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11114006
use warnings;
use Tk;

my $mw = MainWindow->new;
$mw->geometry( '300x300+100+300' );

my $top = $mw->Toplevel();
$top->geometry( '300x300+500+300' );

MainLoop;
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