Hi @Clark_B
Thank you for the detailed response. I followed the steps and confirmed that I already have Automate taxes and forms box checked. It is filing federal and state taxes perfectly, it is just Philadelphia city taxes that it is saying needs to be done manually.
To ensure I have it correctly set up:
In the same menu (Settings > Payroll Settings > "Pennsylvania tax info") there is State tax with my Employer Account ID and then below that a section called Local tax, with "Pennsylvania Local Tax Agency" where my "Local EIN" I put in the Philadelphia wage account # in it. Hopefully that sounds correct.
Thank you.