If you are going to file separately, you should have taxes taken out that way. If you did file Married Filing Jointly, you would get twice the deduction that you do separately, but that is your decision.
If your intention is to have more money withheld from your paycheck, you would claim single.
This would not prevent you from claiming any other status on your tax return.
If you prepare a W-4 for your employer, you can have additional taxes withheld.
On Step 4 Line (c) Extra Withholding. Enter any additional tax you want withheld every pay period.
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