Below is a helpful little script that makes it possible for a provisioning policy (in this case AD) to map the correct DN for a manager:

/*AD Manager*/ 
var adDN = ''; 
var myServiceDN = service.dn; 
var mySupvDN = subject.getProperty('manager'); 
if (mySupvDN != null && mySupvDN.length >0){
    mySupvDN = mySupvDN[0];
    var globalid = mySupvDN.substring(mySupvDN.indexOf("=")+1,mySupvDN.indexOf(","));
    var myPersonSearch = new PersonSearch(); 
    var searchResult1 = myPersonSearch.searchByFilter("Person","(erglobalid="+globalid+")", 2);
    if (searchResult1 != null && searchResult1.length > 0) {
     var mySupv = new Person(mySupvDN);
     var supvUID = mySupv.getProperty('uid');
     if ((supvUID != null) && (supvUID.length > 0)){
         supvUID = supvUID[0];
         var myAccountSearch = new AccountSearch();
         var mySupvAccountList = myAccountSearch.searchByUid(supvUID, myServiceDN);
         if (mySupvAccountList!=null && mySupvAccountList.length > 0) {
             mySupvAccount = mySupvAccountList[0];
             var adDN = mySupvAccount.getProperty("eraddistinguishedname");
             if (adDN !=null && adDN.length >0) {
                adDN = adDN[0];
                return adDN;
             }
         }
     }
    }
}

Here is a list of steps that are being taken by this script to return the AD DN of the manager: Read more