"How many" is asking for an amount, not specifying an operation. It could just as easily be...
How many apples would you have if you started with 5 and someone gave you 2? (indicating addition) or How many apples would you have if you started with 5 and gave someone 2? (indicating subtraction) Other words in the sentence indicate the operation.
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more the yours means to take away
add
Mark up would mean to add. Mark down would mean to subtract.
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.
"How much ... all together ?" usually means add. "How much ... left ?" usually means subtract.