You don't need to split anything into more than 2 parts. FAT32 supports up to 4GB.
MPT works fine with modern loaders and cIOSes without any special settings. You have to save to the real NAND instead of emulated NAND, though. Same with Zelda: Skyward Sword.
MPT works fine with modern loaders and cIOSes without any special settings. You have to save to the real NAND instead of emulated NAND, though. Same with Zelda: Skyward Sword.