1. Each state taxes income a little differently as well. For example, NJ taxes the money you save pre-tax in retirement at the federal level while NY does not. Therefore, you can't do a simple subtraction to get the right wages.
For the NYC wage, that would make sense for your residency wages. Does it look like that includes the NC income, as that would be logical since you lived there during your trips.
Additionally, if NYC includes NJ wages, that is wrong. You don't want to report NJ wages. You may need to speak with HR to get the numbers right.
2. You will prepare NC first and create a NC tax liability. Then when you prepare NY, file for a credit against the NC income that is being double taxed.
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