NeoGeo, CPS1, CPS2 can all use the same core, Mame and FBAlpha (or now known as FBNeo) will run all those games.
Now if you do need to set up a specific game to use a particular core you can use the custom command line for that game, below is an example.Another option if you have a bunch of games and don't want to edit the command line for each game is to set up a new instance of the emulator in LB (it can still point to the old install so no new install of the emulator is required). You set that instance up to use the core you want and then you can just change the emulator being used for each game.