Wad files are installed to the (limited sized) NAND.
Once on the NAND, you can move the data to SD card (using the official SD card menu).
And install more wads to NAND, repeat etc.
At the end, when you will launch a game located on SD menu, the console is temporarily copy the data back to the NAND before launching the game.
if you launch another game, it deletes the temporary files, and copy the new one to NAND, etc.
The USB loaders can display and launch channels only located on NAND. The one on the SD menu can't be launched.
If you plan to have all your games channels on SD and launch them from a loader, then EmuNAND is what you want.
It creates a copy of the NAND to SD or USB, and the loader use that copy as if it was your real console.
You can install as many channels as you have enough free space (2TB partition).
Like you noticed, there are two different emuNAND method:
Neek and cIOS.
neek is a fully emulated environment, all games (almost 100%) are working. but you need to setup neek files, and launch the emulated system menu to launch a channel. The system menu can display only 48 games at the same time.
so if you have more, you can't see them, but neek has a menu to launch additional/hidden channels.
neek (or only neek2o?) has internal patches to set region free and different hacks to the vWii system menu.
the cIOS emuNAND is a redirection done on realNAND.
when the loader launches the game, it reloads to cIOS d2x and tell cIOS to redirect all NAND access to external device.
The cIOS and the environment runs on RealNAND but all NAND access are redirected.
Advantage is easier setup, faster launch and return to loader at game exit. You can list all your games directly from the loaders.
Disadvantage is a less compatibility (75-80% maybe)
The easier is cIOS:
launch USBLoaderGX
go to main menu>top bar>4th icon>enable EmuNAND
go to Settings>features>dump NAND.
go to Settings>features>wad instal to install new games to emuNANDl.
Done !
all is done directly from the loader. dumping, listing, launching, installing wads to emuNAND.
go to Settings>User path>nand path : edit the "EmuNAND channel" path if needed.
set the "EmuNAND save" path to the same location before creating a dump as it's the path that the dump will be created to.
Maybe the issue is not region free? I never tried to launch a channel from another region.
On Wii, modchips can help for region free, but I don't know if channels from other regions need to be patched first vWii.