@adammacks
When you enter the total amount of the extension payments in the federal return it asks what state it was for. In the drop-down list select "Multiple States," at the very bottom of the list. The payment amount will not flow to the state return.
You didn't say whether you are filing New York as a resident or a nonresident. You also didn't say whether you made estimated tax payments to New York. I suspect you did, because that makes it more difficult, but not impossible, to enter the payment with an extension.
On a New York resident return, Form IT-201, the total of estimated tax payments and the payment with an extension goes on line 75. On a New York nonresident return, Form IT-203, the total of estimated tax payments and the payment with an extension goes on line 65.
Go to forms mode and open Form IT-201 or IT-203, whichever one you are filing. In either case, resident or nonresident, if you did not make estimated tax payments the line for the payments will be blank. Just click on the appropriate line and type the amount of the extension payment. Do not double click, QuickZoom to another form, or go to another form in any other way. You can just enter the amount directly on IT-201 line 75 or IT-203 line 65.
If you did make estimated tax payments, the total of the estimated tax payments will be on the appropriate line and you cannot change it directly. Open Form IT-370, which is the extension form. Check the box at the top that says "Check this box to freeze the amounts flowing to this form." You can now change the amounts in the IT-370 Smart Worksheet. On line 1 of the worksheet enter the amount that you paid with the New York extension. If there are any amounts on lines 2 through 5 change them to zero. On line 7 enter zero. Line 8 should now be the amount that you paid with the extension (the same amount that you entered on line 1) and that amount will be added to the total payments on IT-201 line 75 or IT-203 line 65.
