update.pup is a PS3 firmware update file. As for updating the game, acquire the .pkg file containing the update and then install in in rpcs3 through file -> install pkg, so you did that part completely right.
That said I don't actually know how rpcs3 handles, if it even handles, updates for disc games. I know it works for PSN games though (however the PSN version of Dragons Crown doesn't work at all for some reason)
One hack would be to copy the extracted update.pkg (in /dev_hdd0/games/) over the ordinary game files and see what happens. Make a backup first!
That said I don't actually know how rpcs3 handles, if it even handles, updates for disc games. I know it works for PSN games though (however the PSN version of Dragons Crown doesn't work at all for some reason)
One hack would be to copy the extracted update.pkg (in /dev_hdd0/games/) over the ordinary game files and see what happens. Make a backup first!
Asus N55SF, i7-2670QM (~2,8 ghz under typical load), GeForce GT 555M (only OpenGL)