Here's what I did for GCN/Wii backups for USB:
First, make two partitions on your harddrive. I used Partition Wizard Home Edition. The default partition should be NTFS, so leave as is unless Wii backups don't work. Now shrink that partition so you can have another partitioin(I had the new one on the left, not sure if it matters) and format it as FAT32 with 32kB clusters(MAKE SURE YOU DO THIS OR GCN BACKUPS WILL NOT WORK!). Next, get your backups onto the hard drive. I use Wii Backup Manager for Wii games, and DiscEX for GCN. Make sure that the GCN games are in the root of the FAT32 partition, in a folder called games(E.G. root/games/GALE01/game.iso), and the Wii games are in the NTFS folder. Wii Backup Manager should do all the formatting for you.
Now for the wii stuff. I'd go on make ensure you have wad installation privlages(if not, let me know. For now, I'm going to assume you do). I personally use Yet Another Wad Manager Mod. Select the IOS you use for WAD installation(again, if you don't know how to do that, let me know). and install d2x(Use IOS 56 as 249 and IOS 57 as 250). You may want to also install DIOS MIOS while you are on there. I personally use Configurable USB Loader, and you may want to play with some settings first(E.G. make sure it's set to look for an NTFS partition on boot, and that it's not looking for DML, but instead DM).
With that you should be all set, let me know if that works for you.