How do I notify customers if part of their order will be on pre-order?

Pre-Order Manager will automatically notify customers if part of their order is under pre-order. You can change the message at Settings > App Settings

Pre-Order Manager allows you to switch your items automatically to pre-order if they purchased more than the available quantities. Pre-Order Manager will promptly notify the customers if part of their order is under pre-order upon adding the items to cart.

To modify the notification message, go to "Settings > App Settings" and change the value under "Part of the order will be preordered".