You should just be able to look up at the Account's owner like(depending on api name of the master detail account relationship):  
 

    Select Account__r.Owner.Name c,Sum(Invoice_Amount__c)s 
      from Otter_FFA_Invoice_New__c where (Qad_Entity__c=:ent) 
       and (Otter_FFA_Effective_Date__c >=:CurrentMonthStartDate.toStartOfMonth() 
       and Otter_FFA_Effective_Date__c <=:Effective.Otter_FFA_Effective_Date__c) 
     Group By Owner.Name Limit 500