With Data Synchronisation Studio you can now update the Manager attribute with the AD Provider if you modify the Provider configuration slightly.
By default we parse out the Manager field so that it's more suitable for input to SharePoint or something. However you can now switch off this parsing to get to the raw AD attribute value.
To update the manager you need to supply the full Distinguished name value of the AD Object you want to set which would be something like this below.
Disable the TryParseValue and ReadOnly properties of the Manager field in the Property Collection on the AD Provider.
Here I created a Dynamic Column to return the Distinguished Name of the Manager to set against the AD Users.
Now we just create a simple Schema Map mapping the X_Manager to Manager and using DSID as the Key column.
Now you just need to compare the data and synchronise the changes.
You can download and use a fully featured version of Data Sync Studio for 30 Days to see how this AD solution works.