If it were me, and I use illustrator but it might work similarly in your software, I would make the art board a little bigger than the art so I can add the black dots they want for registration. Then put the art in one layer and the cut line in another layer. Then place your black dots, in one layer and copy them to the second layer, illustrator has a feature that lets you put the dots exactly where they are in one layer to the other which helps. Then turn the cut layer off, and save the PNG. Then turn the art layer off, turn the cut layer on, and save the pdf.