I think you may be thinking of the old way of doing things, with the newer versions of retropie you don’t need to modify any paths in es_systems.cfg. rather you can press js0 (button 0 on your joypad) or a keyboard as a ROM loads and you can switch the default emulators on the fly.
But if you’re talking about wanting a two n64 menus in emulation station, one for each emulator yes you’d have to modify the es_systems.cfg.