It doesn't really matter which job you have withhold an additional amount. A $100 of tax withheld is exactly the same regardless of which employer withholds it. That said, if you are more likely to quit or otherwise leave your second job, it might make more sense to have it withheld by them. That way the additional amount won't continue to be withheld if leave and then only have one job. If you used the IRS withholding calculator, you fill out your W-4 according to the way you entered the information in to the calculator. If you indicated multiple jobs and and spouse working for the calculator, you need to check those on the W-4, otherwise the actual withholding will differ from what was calculated.
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