Try adding 2 months to column DATED before analyzing the datepart.
select
customer,
warehouse,
sum(CASE DATEPART(yyyy, dateadd(month,2,dated))
WHEN 1999 THEN val ELSE null END) as y1999,
sum(CASE DATEPART(yyyy, dateadd(month,2,dated)) when 2000 THEN val
ELSE null END) as y2000
from sales table where warehouse='E' or warehouse='EC'
group by customer,warehouse
order by customer