[UPDATED]

First, I just realized this is Access, not SQL Server. I customer sent it to me

Second, I left out qryGroupCert_Base in my OP:

SELECT d.GroupId, 
       Sum(d.cert_complete) AS SumOfcert_complete, 
       Count(d.cert_complete) AS CountOfcert_complete
    FROM (SELECT DISTINCT s.GroupId, e.EmployeeID, IIf(e.Certified Is Null,0,1) AS cert_complete 
    FROM ((Stores AS s 
    INNER JOIN EmployeeStores AS es ON s.StoreId=es.StoreId) 
    INNER JOIN Employees AS e ON es.EmployeeId=e.EmployeeID) 
    INNER JOIN Titles AS t ON e.TitleId=t.TitleId WHERE t.IsManager=True)  AS d
    GROUP BY d.GroupId;

I think that this is probably the right place to do this.

Sorry for the confusion.