TeamTools gets managers for users by looking for a relationship of type “manager” in that user’s record in Google Apps Directory. To see your Directory, go to Contacts and click on the Directory link in the left column. Looking at a user’s Directory entry, you may see a section called “Directory profile”. This section includes data from the Directory, including a Manager’s email if it was set.
The main way in which a relationship of type “manager” is created is by your Google Apps administrator completing the Account information for that user, and filling out the field “Manager’s email.” Note that this field can also be filled in with a name, a non-primary email, an email alias, an email not in this account, or any other text. TeamTools can only map a manager to another user in Google Apps if this field contains the primary email of that user.