Your PA address is your "permanent" address. However, your NY address also factors in on the return. You will list the PA address in the Personal Info tab, but state that your state of residence on Dec. 31 was New York. It asks you if you lived in another state besides New York. You answer yes: PA. Federal Return will be pretty normal. Then you get to the states. You are filing part-year returns for each. Shouldn't have any issues with the PA return. When you get to the New York return, you will see a question if your current address was your address on December 31. You will answer no and input the New York address here. (New York requires this information).
Based on your information, next year you will also file part-year returns for New York and PA (if you live the remainder of this year in PA). However, you will do them in reverse order: you will state that PA is your Dec. 31 residence state, and NY was the other state you lived in.
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