As posted your code is almost unreadable. (When you post code to PM, put it between <code></code> tags. Better yet, become familiar with the contents of the PM site FAQ, especially Writeup Formatting Tips.) Rather than try reading through it, here's a simple file upload script:

#!/usr/bin/perl -T --
use strict;
use warnings;
use CGI qw(:standard);

print header, start_html('Upload example');

print_form() unless param;
print_results() if param;
print end_html;

sub print_form {
  print
    h2('What file do you have for me?'),
    start_multipart_form(),
    filefield(-name => 'upload', -size=>60),
    submit(-label => 'Do it!'),
    end_form;
}

sub print_results {
  my $output_file = '../whatever';
  my $file = upload('upload');
  print h2('Bummer!...') and return
    unless $file and open my $out, ">$output_file";
  {
    my $data;
    print $out $data while read $file, $data, 1024;
  }
  close $out or
    print h2('Not all is well...') and return;
  print h1('Success!');
}
[download]

Make sure that the script has permission to write to $output_file.

Update: Fixed s/param/upload/ in print_results; the original works but the revision uses the "recommended idiom" (see perldoc CGI for a discussion on this).