I don't think I even totally understand your question, but if I do, this is how I would sort of quickly approach it. It's not beautiful, but it works.
  -A

my $container = '/path/to/dir/that/holds/all/the/dirs';
my $tomove = '/path/to/the/dir/you/want/to/move';

my $newdir;
chomp($newdir = `ls -1 $container | tail -n 1`);
$newdir++;
system("mv $tomove $container/$newdir");
[download]

Edit: I just noticed you want to copy instead of move - in that case, just replace the last line with system("cp -r $tomove $container/$newdir");