It depends on how the rest of the question is worded. If it says "how many were left," for example, that means to subtract. On the other hand, if it says something like "how many were added," it means to add.
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add
Mark up would mean to add. Mark down would mean to subtract.
"How much ... all together ?" usually means add. "How much ... left ?" usually means subtract.
none of these
The opposite of add is subtract.