Enter your W-2 exactly as it is shown, including Box 12 entries. The info will flow into your New Jersey return correctly.
If part of your Box 1 Wages are excludable in New Jersey for a particular state issue that is not shown on your W-2, you will be asked about that in your New Jersey State interview.
Click this link for more info on How to Manually Enter a W-2.
For your information, this link gives info on Box 12 Codes.
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