It depends. If the box 1 through 6 amounts (Federal portion) on each W-2 are identical, treat the "separate" W-2s as if they were one. This may be done on the W-2 entry screen by clicking on "Add another line" on the state section to be able to add the PA information.
However, it is also good to remember that NJ and PA are reciprocal states and he should not have had tax withheld in NJ. To get these taxes back, he will want to file a NJ nonresident reciprocal return. All of his income is taxed in PA, but he will get a full refund of the NJ state taxes he paid in.
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