Wii backups can be played from FAT32 or NTFS.
If your drive is FAT32 and your game exceeds the 4GB file limit, your USB loader will split it automatically when installing. I quit using WBFS Manager a long time ago and switched to Wii Backup Manager to handle my Wii Drive transfers, it will also split files at 2GB or 4GB for FAT32 drives.
If you are still using WBFS Manager 3.0, then your drive is WBFS formatted and not NTFS.
If you don't have the capacity to make a backup of your games, there is a program called
wbfs2fat to convert your drive on-the-fly to FAT32, then I used Partition Master to convert to NTFS and resize the partition without data loss. Make the unallocated space fall before your current recently converted partition. Then make that new space a FAT32 partition with 32kb clusters and mark as active.
When I had converted from a single WBFS drive to a split drive, it was to test out NAND emulation but still needed FAT32 partition to be first and didn't have the storage capacity I have now. It took a while for the resizing because it has to move files to free up space at the beginning of the drive. I never tried GC loading but have recently considered giving
Nintendont a try.
WiiFlow, CFG, and GX all support multiple partitions in their latest releases. There is a setting for different partitions on a single USB. WiiFlow is on page 1 of settings, CFG its in settings - system, GX it is settings - Hard drive. And you really should already have a cIOS of Wanin v18 or newer which is when the functionality was made (d2x is on its 10 version and that is the based off Wanin v21).
The
d2x v10 alt added functionality for USB port 1 (port 0 is the default) so you could have 2 drives plugged in and just need to change a setting in your loader to change from one to the other. I'm sure there is a setting for changing from one USB port to the other or use both in GX (also in settings - Hard drive), not sure about the others but probably in with partitions if it can switch. And I guess the Hermes and Rodries cIOS222 had port1 support, which is IIRC where the d2x support came from...