It's best to have a single FAT32 partition formatted with 32k clusters. Then you can have your Wii games loaded, all of your other emulation loaded, and your GC games will work via DiosMios.
DM will only work if the FAT32/32k partition is the first and primary, so best to have it the only.
Proper installation of your Wii games will bypass the 4gig limitation on FAT32 partitions. I suggest reading the FAT32 guide if you have questions. (guide in my signature, in addition to gudes for Dios Mios and downloads needed for it).