Here are all the current methods that you can run a game like BoftW on a custom firmware. I'll bold the method I've been using for months with all my titles without a single issue.
I say "WUP Installer GX2" because it's what I use and I never have any issues (Plus I use the channel version so it's one click from the system menu). There are many WUP Installer's out there though.
1. CBHC -> (Game installed with WUP Installer GX2 to USB)
2. CBHC -> (Game installed with WUP Installer GX2 to system memory)
3. CBHC -> Mocha -> (Game installed to system memory or USB with WUP Installer GX2)
4. CBHC -> redNAND - (Game installed to system memory or USB with WUP Installer GX2)
5. Normal Boot -> HaxChi (hold B) -> (Game installed to system memory or USB with WUP Installer GX2)
6. Normal Boot -> HaxChi -> Mocah -> (Game installed to system memory or USB with WUP Installer GX2)
7. Normal Boot -> HaxChi -> redNAND -> (Game installed to system memory or USB with WUP Installer GX2)
8. Normal Boot -> WebHax -> Mocha -> (Game installed to system memory or USB with WUP Installer GX2)
9. Normal Boot -> WebHax -> HBL -> Mocha -> (Game installed to system memory or USB with WUP Installer GX2)
10. Normal Boot -> WebHax -> HBL -> redNAND -> (Game installed to system memory or USB with WUP Installer GX2)
11. Normal Boot -> WebHax -> HBL -> Loadiine -> (Game copied to SD card and launched through loadiine)
12. Normal Boot -> WebHax -> HBL -> Mocha -> Loadiine -> (Game can be launched from SD or from fat32 USB)
13. Normal Boot -> WebHax -> Loadiine -> (Game copied to SD card and launched through loadiine)
14. Normal Boot -> (launch any CFW using all methods above) -> Loadiine channel -> (Game copied to SD card and launched from SD in loadiine)
13. Normal boot -> (any CFW) -> HBL channel -> (all methods 9 through 12)
Let me know if I missed any
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Ugh such a newb, I am confused now. So I have to have home brew on the system to run wup? Here is my understanding which is probably wrong. I have haxchi on the system, I need to patch the config for the sysnand. Once that is done I can run wup. Can't I run homebrew from haxchi to use wup to install backups?
HaxChi is just a way to launch some other homebrew. It defaults to Homebrew Launcher. Try reading through the first part of this guide. It explains everything:
https://gbatemp.net/threads/guide-noob-guide-to-wii-u-hacking.451297/
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You cannot run WUP Installer without first gaining access to homebrew. You have to have a way to launch WUP installer since that is a homebrew app. You can either launch it from "Homebrew Launcher" or you can install it as a channel. You won't be able to tap the Homewbew Launcher channel though until you are running a CFW.
So follow that guide to achieve this process:
1. Setup HaxChi
2. uplug all USB drives and install CBHC
3. Set up CBHC to autoboot to system menu
4. Launch WUP Installer GX2 from homebrew launcher
5. Install your title
Next time you boot your wii U you only now have to click on the title and it will play. Won't matter if its out of region or homebrew app