If you have already paid them then by all means leave them off your schedule H. There is clearly no point in including taxes you've already paid.
The reason this question has been so difficult to answer is because there is no reason to use the EFTPS system if you are filing schedule H and vice versa. You should pick one method that works for you and use it. Combining the two methods in this way will potentially confuse the IRS and a confused IRS is never a good thing.
@Mnpops
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