You can send messages to both your FBA and FBM (Merchant Fulfilled) orders using the Communication Center. By default, all messages are sent to orders on both fulfillment channels. 

However, if you want to have separate messages for each channel, you can adjust the Fulfillment Channel of your message. This setting is in the Advanced Filters of your message.
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To edit your message filters, please start from the "Automated Messages" tab under Communications in your left navigation. Click the title of the message you want to edit, and then scroll to the bottom of the page and click "Show Advanced Filters" in the lower left corner. From here, you can adjust the Fulfillment Channel as necessary under the "Shipping Filters" heading.

This will allow you to target only FBA or Merchant-fulfilled orders with that message.

Note: If you have orders that are Merchant-Fulfilled to send messages for those orders based on the "Out for delivery" and "Delivered" events, you must integrate the Communication Center with Amazon Seller Central.

Why? Amazon's API does not provide tracking information on Merchant-Fulfilled orders, therefore our system has no way to pull the delivery event information. To enable this functionality, you can follow the steps here: Seller Central Integration Walkthrough.