Yes, you can withhold an extra amount on whoever's check you want to. Did you try doing a dummy return to see if you make out better as Married Filing Separately? If you are having to pay more in this year than ever before, you may want to test both ways before filing to see if you pay less when filing separate. If your income is high enough or you do not have dependents, it is possible that it will help.
Married Filing Joint versus Separate
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