the multiple partition option is for wii games only.
if you want to load gamecube on another partition, you have to go to settings>user's paths>Main gamecube folder : set it to USB2:/games/
remember that nintendont will only mount the first FAT32 partition it finds, so if you have NTFS first, and FAT32 next, it should work.
if you have two FAT32, you need to put games on the first listed FAT32 partition.
Maybe the loader still have a check to prevent users to use anything else than USB1 ? (long ago, only the FIRST partition of the drive could be used, and then only usb1:/ worked, so I made a check to prevent selecting anything else than SD or usb1 partition. maybe that check is still in place. if that's the case, I'm sorry, I forgot to remove it

, or you are using an old version of the loader)
just a thing you should note: you can't have both partition as active, it's not possible (unless writing the partition table manually)
and the wii doesn't care which partition is set to boot first on a computer (Active = tell the computer's BIOS which partition to use to boot your OS from, windows, linux, etc.)
Wii homebrew never check if a partition is active or not, it's not useful and will never affect the compatibility.