This is how I make it work with iPhone & Flash based binary uploads:
Inside the loop you can detect which parameter is actually the name of the upload handle.

my @params = $query->param;
foreach my $param (@params) {
                        my $upload_filehandle = $query->upload($param)
+;
            if(defined($upload_filehandle)) {
                                open UPLOADFILE, ">somePicture.jpg"; 
                binmode UPLOADFILE; 
                while( <$upload_filehandle>)  { 
                    print UPLOADFILE;          
                } 
                
                close UPLOADFILE;
                       }
}
[download]

You should add more validations and logic.