You don't need any tools to transfer Gamecube disc images. Put them in their proper folder and name them "game.iso" and "disc2.iso" for the second disc of two-disc games.
e.g.: "/games/Cubivore Survival of the Fittest [GCVEEB]/game.iso"
If you have two separate partitions like FAT32/WBFS the FAT32 one has to be the first one, I believe. It's easier, as others have said, to just use FAT32 completely. The conversion tool may or may not work with secondary partitions so it might be better to just use Wii Backup Manager to copy them to your PC then delete the WBFS partition and extend the FAT32 one to fill the drive.
Don't use WBFS Manager. It's very old.
ok I'll try that too