You submit both W-2 forms at the same time with the same tax return. If you follow the TTax interview instructions carefully you will see that you start with the W-2 form from the end of the year and then work backwards to the beginning of the year. In other in your case you will enter the New York W-2 information first, then TTax will ask if you had any income from another state, that's when you enter the New York W-2 information.
