You can remap gamepads for each core, it is easy, when in a game enter retroarch and you should see RA's quick menu (if you are in RA main menu go to history, select you current rom and select quick menu). In this menu you can remap buttons for this core or even for an specific game. Also you can adjust other "per core" settings from here.
@Dalton63841 if you lost all your cores make sure you unchecked "Use RetroPlayer installed cores only (Clean cores directory)" in addon settings, this will delete all your cores in every launch in order to use only the ones downloaded using RetroPlayer (upcoming LE9).
Also, if you lost your cores and your DS4 is not working, maybe the problem is that you lost your retroarch.cfg file where both autoconfig & cores folders path is defined.
Make sure after RA installation that you first run it directly before using other frontends, because in RA firts launch some config files and folders are copied to the correct location.
You can take a look to /storage/.kodi/userdata/addon_data/game.retroarch and you should see something like this:
Gamestarter/repository.gamestarter/game.retroarch/retroarch at master · bite-your-idols/Gamestarter · GitHub