Got it. The only amount needed in a NJ state line on your W2 in box 16 is the amount that shows the income that NJ taxes and NY does not (not duplicated). In the federal "Wages & Income" section edit the employer W2 with two state lines and only enter the non-duplicated income amount in the NJ state box 16.
The allocation amount to NJ in the NJ state interview should be the complete wage amount taxable by NJ during your residence in NJ.
For the credit for other taxes paid you are correct. It would be a NJ credit and the income double taxed by NY would be the "A" amount in your scenario (NY taxed income while resident in NJ).
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