Maybe it would be better to have a counter that you increment when you start a thread and decrement when that thread stops. Only start a new thread when this number is below 2. This way when one of the 2 threads finishes you can start another one immediately instead of waiting for both threads to stop

In that case the code should look something like:

my $i=0;
while (@dirs_to_ftp) {
  my $dir= shift @dirs_to_ftp;
  startthread($dir);
  $i++;
  if ($i==2) {
    $i= $i- wait_for_thread_finish();
    $i--;
  }
}
while($i) { 
  $i= $i- wait_for_thread_finish(); $i--; 
}
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wait_for_thread_finish() should return the number of finished threads, since it might happen that two threads stop simultaneously (depends on your modul/library/thread code). starthread() should only start one thread, not two

Now if your real question was how to find out when a thread has finished, then you didn't provide enough information. We would at least have to know: What is your operation system ?
What modul or library are you using to start the threads ?