Format the whole thing using EaseUS Partition Master to FAT32 with 64k cluster size. Trust me, it should work. Just be sure to copy over all your GameCube games first. While I haven't experienced this personally, I have been told that nintendont won't be able to read games beyond the 2TB mark.
Follow the guide I linked to above. It should allow you to format the entire drive to FAT32. Just make sure you use 64k clusters since the limit for 32k clusters is 2TB.