To get the bottom 1000 you will want to order it by a column in descending order, and still take the top 1000.
SELECT TOP 1000 *
FROM [SomeTable]
ORDER BY MySortColumn DESC
If you care for it to be in the same order as before you can use a common table expression for that:
;WITH CTE AS (
SELECT TOP 1000 *
FROM [SomeTable]
ORDER BY MySortColumn DESC
)
SELECT *
FROM CTE
ORDER BY MySortColumn