You owe whatever taxes you owe. If you had insufficient withholding (for any reason) then you will owe a tax payment. It may not be the full $3500 though. Many people have excess tax withheld and get a refund as a result. So the excess from the rest of the year might help cover what you owe.
The simplest thing to do is download form IT-201 from the NY tax web site and fill it out, see how much you owe. If you are going to owe a lot, making an early estimated payment (electronically on the NY tax web site) can reduce or eliminate any late payment penalties.
Turbotax is available now if you want to buy it as a download or CD and use it to make a test return. The online site (which would be free to make a test return but you will have to pay to actually file) won't be open for another few weeks.
