My employer deducted NJ taxes from my salary in 2006. I am filing my taxes and realized that there is a Reciprocal NJ/PA Income Tax Arrangement, where PA residents working in NJ have to only pay PA taxes. State of New Jersey Division of Taxation (http://www.state.nj.us/treasury/taxation/index.html?njit25.htm~mainFrame)

Since my NJ taxes have already been deducted, what is the cleanest way for me to get my money back from NJ and to give whatever is due to PA?

I suspect that the NJ withholding can be applied to your PA taxes, bt I am not sure.

Call the PA Tax authorities for guidance.