Hello
Move your games or backups, by going into the "settings" of the Wii U, then "Data Management", then "move" or "copy" your data or backups or games as you see fit.
I might not have explained my issue clearly enough, sorry for the confusion.
I know how to move/copy data to and from the internal to external hard drive, that is fine.
My issue is that I have my save data on my external hard drive, and the game itself installed on the internal hard drive.
When you go to move data to/from a hard drive you cannot move out only the save data, or only the software or only the DLC, etc. It moves as a bundle.
So moving the software to my external hard drive would overwrite my save file since it'd overwrite the bundle on my external hard drive with the bundle from the internal.
I fixed the issue by deleting the software from the internal. Copying my save data to the internal from the external.
Then re installing Smash to my internal.
The issue arose from me installing the game from a USB drive instead of an SD card because my SD card couldn't hold the whole game to install, so I needed to install it to nand.