Blackboard has always included a course messaging system which allows users to send messages to other course users which remain internal to Blackboard. These messages are not the same as email; course message and email are separate tools but both remain available inside of courses in Syracuse's .
The biggest difference with Blackboard Ultra Navigation is that messages sent in courses are now consolidated and displayed on the main navigation menu. Users will see a badge with a count of unread messages. Clicking on "Messages" will display a list of current courses and organizations where you can click to access the course message or click the plus button to create a new message.
More information about Messages is available from Blackboard.