I partitioned a 500gb Seagate Freeagent Go to where the first partition is FAT32 (for homebrew, emulators, etc.) and the second partition is WBFS. I used a free program called Compuapps Swissknife to delete the whole drive partition first, then created the first partition as FAT32 set to ACTIVE and primary. Then I made the second partition FAT32 primary. After making sure that Windows assigned each partition a proper drive letter, I used WBFS Manager 3.0.1 to format partition 2 to WBFS. I'm using Windows XP sp3.
This method has worked perfectly for me, and all homebrew on the FAT32 partition works perfectly. I prefer WBFS, simply because it compresses the ISOs when added, allowing more games on the drive. I haven't read much on loading Wii ISOs from a NTFS partition, but I imagine that you'd have to scrub each game if you wanted fit the same amound of games as a WBFS partition. Could someone correct me if I'm wrong?