Fan translation teams (such as the prominent updates from the Vanguard community on platforms like GBAtemp) usually prioritize card functionality over story mode.
Which in the trilogy are you trying to set up? cardfight vanguard 3ds english patch repack
Power off your 3DS, remove the SD card, and insert it into your computer. Copy the .cia file into a folder on your SD card (creating a folder named "CIA" keeps things organized). Fan translation teams (such as the prominent updates