Ok ... let me take a step back and explain your situation.
First ... You should just pay the original balance due you already owe so the IRS doesn't get confused.
Then when the amended return can be filed you will pay the extra that you owe with the 1040X before 4/18.
After you amend the federal you can complete the original NY return and file it correctly the first time. Do not make any changes to the return before you can use the amendment process sometime in Feb ... doing so will mess you up badly. Right now you really need to just sit tight and be patient... rushing is how you got in this mess to start with.
