より良い方法があることを願っていますが、2つのサブクエリを交差させるか、しないことでこれを取得できます：
Select mytable.Store, mytable.Dept, mytable.Order, mytable.Amount
from mytable m
inner join
(Select Amount from mytable n where m.store = n.store and m.dept = n.dept order by Amount desc limit 2) as high_enough
on mytable.Amount = high_enough.Amount
left join
(Select Amount from mytable n where m.store = n.store and m.dept = n.dept order by Amount desc limit 2) as too_high
where too_high.Amount is null
group by Store, Dept;