You would have to make the FAT32 partition first on the drive. Make sure to use 32k clusters and set it active and primary. Even then there's no guarantee, as some drives just don't get along with DIOS MIOS.
This means that to get FAT32 on the drive before your existing NTFS partition, you need to either wipe out the whole existing drive and repartition it, or use a non-destructive partition tool like Paragon Partition Manager to move your existing NTFS partition further back on the drive and make the new FAT32 partition. BACK UP ANYTHING YOU CAN'T AFFORD TO LOSE BEFORE DOING THIS. Even nondestructive partition software sometimes can have a a hiccup or whatever and you don't want it wiping out something you can't get back.
FAT32 is not really limited to X-amount of gigs for the drive (so long as you're not using MS's own formatting tool), just for individual file sizes. Splitting Wii games in to 4GB chunks in Wii Game Manager would let you run everything from a single partition and you'd still have to repartition/reformat if you wanted to go that way, but that's up to you.