Board Thread:Questions and Answers/@comment-71.92.104.236-20130704060736/@comment-5627887-20130704120624

When you put one underground, it will appear on the level you put it at, delete an area for the quarry frame to fit in (you won't get any materials from the area it deletes), then start at that layer and work downwards as normal. It won't start at the surface. Putting a Quarry underground can be good to hide it, however the initial deleting it does to clear a space for the frame could destroy ore that you would have rather mined, so you can get around this by mining the area it will fill manually beforehand.