I have not had a problem.  I successfully attached a copy of a client's W-2 to the PA return due to an "incorrect" withholding amount.  I allows me a choice of Pennsylvania, Philadelphia BIRT, or Philadelphia NPT in the drop down box.  However, I have not e-filed the return yet. 

If you can't get it to work, I would recommend e-filing the return as planned and faxing or e-mailing the additional information to PA.  I'm trying to avoid filing anything on paper due to the combination of postal delays and processing delays at PA DOR.