Typically, NJ will want you follow the same calendar of residency that was reflected in your federal return. So if one of you files as a resident of NJ, NJ wants to know the entire family income so they can tax your family at a higher rate before crediting back the non-NJ income. That is how NJ gets a bigger cut. Don't forget to check to see your spouse's non-NJ income comes from a state with reciprocity with NJ (like Pennsylvania). Reciprocity changes the rules with respect to what has to be filed and what income needs to be included on the return.
It is all very complicated and you may need to calculate different scenarios before you finalize your federal and state returns. In my case I had to spend some quality time on the phone with the NJ tax office and the offices of the other state(s).
