That's not how it works. There are so many things wrong with this post.
1. WUDs are raw disc dumps, just like ISO. It's just the file extension chosen for Wii U dumps, it has no significance.
2. WBFS Manager AFAIK only works with WBFS formatted drives. You need to use Wii Backup Manager for FAT32 drives.
3. WBFS is for Wii games, not Wii U games. WUPInstaller can't read them.
4. WUPInstaller can't install ISOs, the games have to be converted to .app format, this can be done with nuspacker but it's a bit of a hassle, even if it takes a while it's probably better to download the games in the original .app format with an app like Wii U USB Helper.
5. WUPInstaller can't install games from USB drives anyway.
Bottom line, a 32GB+ SD card is almost required for using WUPInstaller, as some games can be over 20GB in size, and WUPInstaller will only install from the SD card. There is a workaround to this (Mocha FAT32 HDD as SD card beta -> Install games from FAT32 USB HDD to internal memory -> Reboot and move games to Wii U formatted HDD) but you need a 32GB Wii U with lots of free space.