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Hi from just answer. I'm PDtax.
You could just amend the filings, and cut a check to pay in the back taxes. This skips the EFTPS system. I might consider another way.
Pay all the pay at once, prospectively. Deposit through the EFTPS system as if all the work was done in December.
The amendment and check is the correct method, the catch up method could be considered acceptable. The second method likely escapes the penalties.
Thanks for asking at just answer. Positive feedback is appreciated. I'm PDtax.