It depends. NY has a Convenience of the Employer Rule that would need to be met in order for your son to not pay taxes to NY. If your son meets the criteria for the Convenience of the Employer Rule, then yes, you would file $0 for the NY return, then file the PA return and pay taxes on the income in PA.
If this is the case, then he should contact his employer and have them withhold taxes for PA instead of NY.
If your son does not meet the criteria in the link above for the Convenience of the employer, then he is subject to NY taxes and would need to pay tax on all the income he earned working remotely for the company based in NY.
He would then get a credit on his PA taxes for the taxes he paid on the income earned in NY. He would still need to include ALL income on his PA return.
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