In case anyone else stumbles upon this thread:

The Order Manager module uses an Order Integrator app that sits on your desktop and syncs with your zen db. You can download your orders to the desktop, enter comments tracking numbers etc, then it will upload to your cart and email the customers. It's still one at a time but it's a bit faster than adding a lot of tracking numbers through the zc admin.

Zen Cart Order Manager:
http://www.zen-cart.com/index.php?ma...roducts_id=223