W2 for Puerto Rican Employee

I have one employee out of 2000 that is a resident of Puerto Rico but actually works mostly in Louisiana.   I am having problems generating correct W2s and/or 499Rs for him.  The probllem is that he has had federal taxes taken out since he worked in Louisiana.   The 499R doesn't reflect the Federal wages, and I can't print a W2 since he is coded with Tax Method R for Puerto Rico.  Can someone point me to a document that explains how to get the information onto the W2 and/or the 499R.   Also the electronic file for SSA does not include this employee