Deducts subtract openings and cut-outs from areas — the totals you see are always net.
A deduct is not a negative line item. It is a shape that carves out of any area it overlaps on the same sheet, whatever item that area belongs to — a window opening out of a wall, a stairwell out of a floor, an island cut-out out of a slab.
A floor measures 355.42 SF. A 14.83 SF stair opening is drawn as a deduct. The floor's stored quantity, its label on the plan, the panel, and the Summary all read 340.59 SF — the deduct itself appears nowhere as a line item.