You can't just use WBFS for everything. If you made a FAT32 partition you could put every homebrew app and all your nes, snes, n64 roms on that partition without trouble. I suggest you to backup all your games to your PC and format your external HDD to FAT32. keep your HDD in FAT32 format, and put your games on it using wii backup manager or any other tool. That's the easy way. if you really want a WBFS partition, than you should look for a guide about partitioning your HDD.
edit: I forgot to tell you that the WBFS partition is only meant to be for wii games.