They PA and NY returns are separate returns. When you answer the Personal Info section questions, one question will ask if you worked or earned income in any other state. Just answer yes to that question. Then when you get to the state section TurboTax will walk you through the New York and then PA returns. You want to do your Non-Resident return before the resident return so you can get the credit for taxes paid.
No, you cannot have extra withholdings for PA. PA is pretty cut and dry. The tax rate is 3.07%. Generally, NY state tax rate is higher than PA's so chances are you won't owe anything on the income earned from NY to PA because of the credit.
If you file a federal joint return with your husband, you would generally file the joint returns for the states. If you file separate, you would file separate for the states. However, since you are both non-residents of New York and only you have NY source income, you do have the option to file a joint Federal Return and a separate NY return.
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