While the Communication Center does not currently have an optimized way of working with multiple brands for the same seller account, there are still ways to target these brands individually:
Email templates can be specified to only send for certain ASINs or SKUs from the Filters tab of each message, allowing brand specific customization per template. Learn more about item filters here.
From the content of your message you can also add the brand logo, allowing a different logo per brand for each message where needed. The image button is located along the top of the message editor toolbar, and looks like a landscape icon.
Be aware that all messages sent through the Communication Center go through Amazon’s Buyer-Seller messaging system. The messages originate from the Communication Center and are sent to Amazon’s email system using the special email address that you see for the buyers (they look like firstname.lastname@example.org). Amazon’s system will then put your Seller name, and a similar, cryptic-looking email address in the "From" address, and send that to the buyer. As a result, the messages sent through the Communication Center will always have your proper Amazon selling name when viewed by the buyer.