Hacking Partitioning Questions

[cots]

I want to partition my 1tb USB drive so I can have my Wii games on the first partition and my ROM collection on the second, but when I partition the first with fat32 and the second with NTFS Wiiflow won't see the Wii games on the fat32 and the emulators won't load from the NTFS. I've seen you can format a WBFS partition so what should I do so I can play my Wii games and emulators? The reason I need a NTFS partition is due to the fact some of my Roms, well actually a lot of them are >4GB.