Folder level tracking allows for automatic tracking of emails based on the folder that an email is in. The email will be automatically regarded to the record that is mapped to the folder.
An administrator must enable folder level tracking as a system setting and then each user that wants to use the feature must configure folder tracking rules in Personal Options.
Folder level tracking requires Exchange and Server-side synchronization.
Other limitations include a maximum of 25 folders that can be tracked per user.
More details here, https://technet.microsoft.com/en-us/library/dn946907.aspx