It is not paid separately. The MCTMT is a part of the NY return and shows on line 54b. It is part of your total tax on line 61. The payments you have made should be included on line 76.
Your refund shows on line 77.
Since you have a refund, the program must have been letting you know about the MCTMT being a part of your return. Please verify with your return that this is the case. Let us know if you need more help.
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