Ok, so here's what I have now:

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 AND e.IsActive=True)  AS d
    GROUP BY d.GroupId
UNION ALL SELECT 0 as 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 AND e.IsActive=True)  AS d;

I'm no longer getting prompted, but it's not filter out inactive employeed either. I don't see what's wrong.