Okay, CT-3-S is stating that you owe $13 for 2019, in order to pay it, you are being asked to use the payment voucher CT-200-V to submit your payment. Apparently, New York does not know about your Direct Debit.
The Form CT-400-MN is for you to pay Estimated Taxes for 2020 tax year. You can simply send a check for $13, or split the payment into quarterly payments, the choice is yours.
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