I used to do this decades ago before personal computers/software. I worked in PA and lived in NJ. If I remember correctly, you paid to the jurisdiction where you worked and got credit for that in the state in which you lived. Have you downloaded paper forms from PA/NY? Frankly, it might be easier to figure it out that way. In re-reading your initial post I see hubs get income from both states. Used to be - if I remember correctly - you paid the tax to the higher rated jurisdiction and then got that credit against the tax in your residential state. Could have changed/I could not be remembering correctly.
Since we opened an LLC several years ago now we have a private accountant do our taxes. Worth the fee as over those years we've gotten generally triple back what we paid in fees. Depreciation and all that sort of stuff that was far more complicated than I wanted to be bothered with at that point.
I tried Turbo Tax a number of years ago and, frankly, was underwhelmed. It asks you specific questions at the beginning of the process and if you don't exactly know the answer, you don't necessarily get the proper questions/line items that you need further down the line. Dinosaur that I am, I stuck w/paper when I was doing our taxes myself. Can't speak about the H&R software. Good luck.