I've been a Papers fan for a few years, but recently, after getting my Kindle, I missed a few features, such as, moving PDF books to the Kindle and changing certain PDF books to fit the Kindle MOBI format. Also a nice feature is browsing covers. In addition I wasn't quite satisfied with how Papers fetched meta data for books - only supporting Google Books was a draw.
I tried calibre for a few days. My biggest concern was how to move my neatly organized library to calibre. Matching all the books (about 1400) in Papers had taken forever - or at least a few days. Doing it again, book by book, was never going to happen. Luckily I found out the 'batch download meta function'. And it has worked great. After some trial and error, I found the following workflow the most effective.
First of all I don't want to import all my academic papers, so, in Papers, I sorted by Journal, selected all without any, and added them to a collection. Then I selected the right collection (File->export>PDF files->tick 'Selected Group') and exported it to a new folder. I've set Papers to change the PDF filename to 'Title_Author' (Preferences->Library).
I then launched calibre and set it to read metadata from file names rather than file contents when adding books (Preferences->Adding Books->make sure 'Read meta data from file contents rather than file names' is NOT ticked).
I then had a library with the title columns containing the title and the author, while the other columns were empty. I tried to copy paste the author name to the author column and also to delete the author name, but I found the greatest success rate (90 percent) simply leaving it as is. Not to overwork the app and to try different ways I fetched meta tags for 100 books at a time (Select the books and hit command+d...on a mac).
Fetching meta data for 100 books takes approximately 20 minutes. I then go through the books one at a time checking if the right meta data has been fetched (select a book and hit 'v', and the file opens up, very snappy, in Skim, if you have that installed. Then escape and go to the next one. If it's not the right one, hit 'e' and do it manually). With an error rate of 10 percent it takes about 10 mines.
Checking and correcting the meta data for 1400 books took me a little over 2 hours. Fetching the metadata about four and a half hours - these can be spent doing something else. For me, reading on my brand spanking new Kindle.
Overall, it was quite a painless transition. And I am now a happy calibre user. Have a nice day.