The employer already made some determination of the wages earned in NY by withholding only $3,000 of NYS tax.

I have several clients who work for consulting firms and might work in various states throughout the year. They live in NJ, so all wages are taxed to NJ.

NY always starts at 100% of federal wages, Box 16, but the tax in Box 17 is too low for 100% of the wages. On the IT-203 you can enter the NY wages, such as if the NJ resident worked at home for part of the year. Only the NY piece goes on the NY column of the IT-203.

Some employers are putting the NY wages in Box 14 of the W2. Some call it "NYWAGE."