How to connect multiple HDDs at the same time on WiiU
at least one for WiiU games, and one for vWii homebrew​

Why do you need a guide to plug two HDDs?
The "two HDD at the same time" issue is usually an issue only with Nintendont+USBLoaders.
WiiU+USBLoaders were never an issue.
WiiU+Nintendont was an issue, but could be fixed by switching the USB order.
What is/was the issue is using both USBLoaders and Nintendont while having a WiiU HDD plugged at the same time without swapping manually based on which game you play(ed).


this guide is kind of obsolete now.
Since Nintendont 5.460, Nintendont is skipping incompatible USB devices.
Meaning it will NOT see the WiiU hdd at all. It's like if you have only one drive connected.


2 HDDs setup
This setup use the same HDD for Wii and Gamecube games.

So, now, the only guide you need is :
Plug your Ustealth vWii HDD to USB Port0 (the top back port)
Plug your WiiU HDD in any other USB Port.
Done !

Enjoy all your wiiU capabilities.


The different (old) guides

There are two methods (at least).

All the basis under this is that cIOS and IOS58 are mounting USB in different orders !
cIOS are mounting USB in incremental order, and only one port is enabled at a time: USB Port 0 then USB port 1 (usb libraries were never updated to check highest ports)
IOS58 is mounting USB in decremental order, and all ports are available at the same time : USB Port 3, USB Port 2, USB Port 1, USB Port 0

Information about gamecube games:
This guide let you use HDD to play Gamecube games.
This guide expect you to use an USBLoader for both Wii and Gamecube games, therefore you have to use FAT32 for gamecube games. ExFAT works with nintendont but can't be used inside USBLoaders. If you use exFAT, don't use USBLoaders and launch nintendont directly. If you use exFAT, this guide might have too many steps for you, as it let contains information to display gamecube games.

You are not forced to use Gamecube games on USB, you can use SD card for Gamecube games ! adapt the guide to your liking.


2 HDDs setup
This setup use the same HDD for Wii and Gamecube games.

hardware
Hide your vWii drive using Ustealth Windows app, or USBToggle vWii homebrew, or linux/macOS dd commands.
Connect the WiiU HDD in lower port number (in fact, Port0 only, top back on WiiU)
Connect the vWii HDD in Port 1 (bottom back on WiiU)
Connect Y-cable if your HDDs are not already externally powered to remaining USB ports, or external USB power sources. You can use a HUB connected to one of the front USB port to get additional y-cable power for 2 HDD, and keep an empty USB Port for gamecube adapter or controller's charging.

software
Install cIOS d2x v10-alternative r53 base 57
Setup the slot number you installed that IOS in your Wii USB Loader setting, do not use d2x r52 at all. set it to both loader's IOS AND game's IOS.
In USB Loader settings, if required, select the USB Port to use (example in USBLoaderGX : settings > HDD menu > port : 1)
If the loader doesn't find your game, maybe it still register the WiiU HDD as "first partition" (usb1:/). in that case, set the path to your Wii ISO games to the proper partition number (might be usb2:/wbfs/ for "second partition")
example in USBLoaderGX :

Settings > HDD Menu > install partition : click to select the partition where your Wii games are located​

result
- WiiU will not see the vWii hidden drive and will use WiiU HDD.
- Wii USBLoaders will skip the WiiU HDD (not a recognized format), and mount the first found compatible partition : Port0 (skip) > Port1 (partition 1 to 4)
- Nintendont will mount higher HDD in priority : Port1 partition 1 (that's all, only the first found FAT32 or exFAT partition)
- Other homebrew using IOS58 should work the same as nintendont.

Cons: Wii games require cIOS d2x r53 base 57 to enable Port1, which has less compatibility than r52 for Hardware and software. (emuNAND might not work, some games won't work like Just dance 2016, Wii games on SD will not work)
Pro: Easiest setup, it works with 2 HDDs, no need to unplug anymore, no need to heavily change and edit loader's settings, (should) works with ALL vWii homebrew.

Issue: if your HDD is not detected by USBLoaderGX, open the meta.xml in a text editor, delete commented lines if still present, and manually set --ios=58



3 HDDs Setup (requires additional USB HUB device) (thanks to balteck for this idea and testing)
This setup use different HDDs for Wii and gamecube games.

hardware
Hide both your vWii drives using Ustealth Windows app, or USBToggle vWii homebrew, or linux/macOS dd commands.
Connect the vWii HDD with Wii games in port 0 (top back)
Connect a USB Hub on port 1
Connect the WiiU HDD in the HUB's lower internal port number
Connect the vWii HDD with Gamecube games in the HUB's higher internal port number ! important !
Connect Y-cable if your HDDs are not already externally powered to remaining USB ports, or external USB power sources.

software
Install cIOS d2x v10 r52 base 57 (NOT v10-alternative r53)
Set the Wii USB Loader to use IOS58 inside the loader, and the slot number you installed the cIOS d2x v10 for game's IOS.
setup USBLoaders to mount multiple USB Ports
Setup USBLoader path to properly load Wii and Gamecube from their correct path (usb1:/wbfs/ usb2:/games/ etc.).
example in USBLoaderGX :

Settings > HDD Menu > install partition : click to select the partition where your Wii games are located
Settings > HDD Menu > USB Port : both
Settings > HDD Menu > List all partitions : Enabled
Settings > HDD Menu > Gamecube Main path : usb2:/games/​

result
WiiU will not see the vWii hidden drives and will use WiiU HDD connected to HUB.
Wii USBLoaders using IOS 58 is compatible with HUB. It will skip the WiiU HDD (not a recognized format), and mount the compatible partitions in this order : Port1 HUB 1 (Gamecube games) > Port 1 HUB 0 (WiiU, skip), Port0 (Wii games)
Wii games using cIOS will mount in incremental order : Port 0 (Wii games)
Nintendont will mount higher HDD in priority : Port1 HUB 1 partition 1 (that's all, only the first found FAT32 or exFAT partition)


Cons: you need a HUB, you need 3 HDDs, maybe you need lot of power supply too, but the hub will give you extra power slots for Y-cables, You need a lot of user setup and understanding how loaders are working!
Pro: it works with d2x r52 base 57, which has better hardware and software compatibility than r53 with a 2 HDD setup !

Issues: None?

Why it works fine :
cIOS mounts drives in increasing order (USB Port 0, then USB Port1), but r52 doesn't work with HUB so it will see only Port0.
IOS58 mounts drives in decreasing order (USB Port 1 hub 1, USB Port1 hub 0, USB Port 0), so :
- nintendont (and other homebrew using IOS58) will mount the first encountered HDD from the HUB with gamecube games
- USBLoader interface (using IOS58) will mount the first HDD with gamecube, skip WiiU HDD, mount the second HDD with Wii games
- USBLoader will reload to cIOS and only port 0 will work to play games on the first found HDD in port 0
- WiiU will skip the two stealth'd vWii HDDs and see only WiiU in HUB.



BONUS : 2 HDDs Setup (requires a non lazy human)
Get up and walk to your console to plug only ONE drive at a time based on the game type you want to play (WiiU or Wii/gamecube)

Cons: you need to get up from your couch
Pro: You do sports! you lose calories, you become less lazy, IT JUST WORKS !

Issue: If you don't want to get up, ask your sister, brother, family member to do it for you.


EXTRA BONUS : 1 HDD Setup (requires a non lazy human)
You can have WiiU games installed on a FAT32 partition when using a beta version of Mocha.
This way, you can store ALL your games on the same drive : WiiU, Wii, Gamecube

This is easy to setup, but requires a lot of steps each time you want to install a WiiU games.

To use this setup, you need a temporary WiiU HDD (required once).

hardware
Source HDD : any compatible drive to use as WiiU HDD. can be a small flash drive.
Target HDD : any FAT32 drive you use for vWii (and soon, WiiU too). 2TB partition max?
DO NOT HIDE your drive using Ustealth. if hidden, unhide it with Windows app, or USBToggle vWii homebrew, or linux/macOS dd commands.
Format the Target drive to a single MBR primary FAT32 partition. Important ! WiiU only mounts MBR Primary, not GPT, extended or logical partitions, and only FAT32 not exFAT.

Software requirement - working setup (installing game)
- CBHC or Haxchi OR Mocha (non beta)
- FTPiiU Everywhere (haxchi version should work with Mocha too) + Computer's FTP Client
- WUP Installer
- Game in Encrypted format
- Game in Decrypted format
- Enough space on NAND to install the game

Software requirement - deployment setup (playing games)
CBHC installed and setup to boot Mocha by default
Mocha beta located in SD:/wiiu/apps/mocha/mocha.elf
All other WiiU homebrew located on USB:/wiiu/apps/ (the USB becomes the SD ! SD is not available anymore after Mocha is loaded)

Preparing the USB
- Connect Source HDD and format it to wiiU format.
- if not using CBHC, Launch Haxchi or Mocha (non beta)
- Launch FTPiiU everywhere, and connect using a FTP Client
- Browse to USB and copy everything to computer
- On Target FAT32 partition, create a new folder on root named "usr" (if not already dumped from ftpiiU)
- Copy all extracted WiiU HDD data into the /usr/ folder

Source HDD not needed anymore.

Installing game to FAT32
annnnd no, you can't use WUP installer directly to FAT32 !
Mocha is beta, it doesn't have necessary library's function to convert WiiU file permission to FAT32.
You can't move game from internal to FAT32 using Data management menu either !

- Install encrypted game to NAND (not USB) using WUP installer of your choice !
- Copy Decrypted game to TARGET FAT32/usr/ folder (in the correct sub folder based on game's TitleID) *will add proper path later*
You can decrypt the game using one of the NUS decrypting tools, or one of the NUS downloading tool in decrypted format, or even FTPiiU Everywhere by getting the game from NAND!
- Delete the game from NAND using the settings > data management (game data not needed anymore, the ticket will remain and has marked the game as "game installed and launchable")

Cons: you need to install to NAND first, then delete the game from NAND. Some feature might not work (savegame creation? folder creation ? as Mocha FAT32 beta is missing WiiU commands interpreter)
Pro: you can use FAT32 ! only one HDD !!

Issue: You already had savegame and dlc on your NAND? you need to move them to USB too !
Note: Maybe you can do FXP (copying data from NAND to USB without going through computer), as it's the same source, maybe "copy /source /target", or even move instead of copy.
Note: if you don't launch Mocha directly from CBHC, the WiiU will ask you to format the drive ! DON'T !
Note: USB has priority over NAND. If you have a title installed on both, USB will prevail (savegame on USB, DLC on USB etc.), data on NAND will not be used/replaced/updated when playing the game from USB.