You can use either assuming you have the concentration and volume to calculate the number of moles (work through the calculation with both to satisfy yourself that you get the same answer). If the question tells you that one of the reagents was added in excess, then obviously don't use that number of moles.
How do you know what moles to use in the second step? Like if my ratio is 1:2, how do I know whether to use the acid or the alkali
You can use either assuming you have the concentration and volume to calculate the number of moles (work through the calculation with both to satisfy yourself that you get the same answer). If the question tells you that one of the reagents was added in excess, then obviously don't use that number of moles.
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