If you imported them to work with retroarch you need to bulk edit the games to use another emulator.
Do you have a MAME fullset? did you use the fullset importer?
I dont currently, but have used a dual shock 4 with both ds4 windows and input mapper and they always worked just fine.
nowhere ever have we claimed that, Launcbox, as you may tell from the name is a launcher, you tell it where your games are and where your emulator is, Launchbox then passes the game via commandline to the emulator. If the emulator requires setting up to some extent, which some do, then that is on you im afraid. As i said Launchbox has no more interaction with the emulator other than passing the rom to it.