In the Unix world, it is standard practice to specify command-line options when you are invoking an application, especially a graphical program. Starting your program as myscript -geometry "80x40" would not be unusual. To have Perl/Tk parse and apply these command-line options for you automatically, just call CmdLine immediately after you create your MainWindow.
$mw->CmdLine;
For complete details, see Chapter 16, "User Customization".