The PS3/PS4 both share the same controller, which is named PS4. This controller should work for both the Playstation 3 and Playstation 4 with a few caveats. Most of the buttons will work, however, some of the controller specific buttons do not work.
After pairing your remote, simply remove flirc from your PC, and put it in your PS3/PS4. It should work with your previously paired remote without any additional settings.
Because Flirc emulates a keyboard, some applications wont work. Some applications only work with a PS3/PS4 approved controller.
We are working diligently to circumvent this, and a solution is in active development. For more information, to follow development, and to try out beta images, subscribe to the forums and follow the discussion here.