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