Just change the state section on the W-2 Wks.  So if the W-2 says $50,000 MD Wages & $3,000 MD W/H but you know (from paystubs) that only $30K of the wages were earned while the taxpayer lived in MD and the other $20K while the taxpayer lived in PA you'll change it to:

MD $30,000 Wages, $3,000 W/H
PA $20,000 Wages, $0 W/H

Then things should flow to your PY Allocation Wks correctly.

Rick