The container mapping is used to define the container (or org unit) that the user will exist in.
A common setup is to state that when Connect to AD creates a new user in Active Directory, it should create the user in a specific container. Also, it should not change the container for existing users.
This can be achieved by using a conditional expression on the Container mapping that indicates that new users go into a specific container and existing users should not have their container changed (it should be ignored).
New users will be created in the New Users org unit.
Existing users will remain in their current container because the conditional expression states to Ignore this mapping (their container will not be changed).
Keep in mind that you have more control over this mapping and you can easily define additional conditions to handle more complex conditions as seen below.