If you have finished importing your Papers 3 library then the New Papers should have all of your PDFs and you are well on your way to continuing your life of research. Since some people have massive Papers 3 libraries we leave the PDF's in their original locations and upload them from there. Since the files are linked any changes you make in the new papers will break Papers 3 and any changes you make in Papers 3 will break the new papers. The applications are not linked and should not be treated as such. If you wish to use both at the same time you can try backing up your Papers 3 library into a different location and using it from there but this is not recommended.