Starting with version 126.96.36.199 and above of AD Bulk Users you can set a users manager value using the managers username, distinguishedName or the managers employeeID.
Internally in Active Directory a users Manager (seen on the Organization tab) is stored using the managers distinguishedName, for example:
With version 188.8.131.52 and later you can use the distinguishedName, sAMAccountName (username of the manger) or the employeeID.
Below are three example CSV files that would set a users manager value.
pjones,True,jblunt (using managers sAMAccountName)
pjones,True,123987 (using managers employeeID)
Using the sAMAccountName or employeeID will be slower than using the distinguishedName as the program will need to query Active Directory for the managers distinguishedName value.