Why not just make the whole thing FAT32? All the wii apps will work with that, the only problem is you can only put files that are smaller than 4GB on it (not a problem for wii stuff, but if you are putting a big movie or something on it, you will have a problem).
The other option is to use NTFS, in which case not all wii apps will be able to use it (USB loaders can though).
Or you could partition it to something like this:
4-8GB FAT32 (keep wii apps and stuff here), and the rest NTFS (for wii games and all your other files.)