Your NY return is a resident state return and taxes all income. Your PA will need to be a nonresident return claiming only the PA income.
NY gives you a credit for PA tax paid. Your NY tax return could not be accurate without the PA tax liability. You will need to finish your PA and then wait until NY is finished and processed. NY might realize your return is incomplete and stop the original so that you can correct it rather than filing an amended return. If it does get processed, you will need to file an amended return with NY.