My typical command line parsing goes something like this:

use vars qw/ $opt_help $opt_one $opt_two $opt_config /;

sub parseCommandLine();
parseCommandLine();

......
......
sub parseCommandLine() {
  &getOptions( 'help|h', 'config|c=s',  'one', 'two=s' ) or $opt_help 
+= 1;
  
  if( defined( $opt_help ) ) { 
    &printUsage();
    exit(0);
  }
  
  if( defined( $opt_config ) ) {
    &parse_config( $opt_config );
  }
  
  if( defined( $opt_one )) {
    # do extra setup required for option 1
  } else {
    $opt_one = 'default_opt_one';
  } 
  
  unless( defined( $opt_two ) ) {
    $opt_two = 'default_opt_two';
  }
  # Do stuff needed for option 2.
}

sub parse_config(  ) {
  my $config_file = shift();
  # read file
  # use file to set $opt_one, $opt_two
}
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Hope this helps...Untested code of course :)