I want to have two separate games of Ultra Moon, but I only have one console. If I have two copies of Ultra Moon, will they have different progress if swap them in the same 3DS?
According to Nintendo, all 3DS games are saved to the cartridges they are played on (unless they are games downloaded from the eShop). The only information saved to the 3DS system itself by some games is StreetPass and SpotPass info.
Pokémon Ultra Moon is no exception, all information is stored on the Game Card.