Reciprocity MD and PA: Reside in both MD and PA, tax resident of MD, work is in PA and income comes from PA job; employer withheld state income from both states.

I am filling non resident return for PA to ask refund and planning to file resident tax for MD. The software does not seem to acknowledge the tax reciprocity.
Question : How do I use the software to get refund from PA as PA non resident or are some income tax required to PA because the employer is located in PA, despite the fact that I am tax resident of MD and normally should only pay taxes to MD even if I work in another state (with a reciprocity agreement)? In the software, I am to pay additional PA taxes instead of getting a refund. 
I have not yet started the MD return since it’s advised to do the non resident return first. Please help