This is relatively short and sweet, so long as you already have Wii U: Breath of the Wild game & Update Data dumped to your PC or removable media (SD/USB Drive).
The game must be in LOADIINE / RPX FORMAT. This means the entire game consists of only 3 Folders: CODE, CONTENT, META
Setting up CEMU & Games:
Please view my other guide on CEMU's Wiki for setting up CEMU: Click Here
a. Installing Mods that include the directory:
Installing the mods that have the Cemu mlc01 directory by default is extremely simple. Make sure to keep a backup of the Update Data stored somewhere for later use. This is for if you wish to revert changes made by mods.
Some mods posted will already have an mlc01 Folder to extract into your Cemu directory. When you are asked if you would like to replace the files, accept all of the changes.
You're now ready to load the game in Cemu. Be aware that there may be some graphical glitches while the mod renders into the game. This should only last around 10~20 seconds.
b.Installing Mods by hand, into the directory:
(Make sure to keep a backup of your Update Data to allow you to revert changes!)
Some mods may come in packs or may lack the directory structure in order to just drag and drop them into place. You may either want specific mods out of the pack or you might have to put the mods into the directed folder on your own.
Open up your BotW Update Data directory, then open up the Content folder. This is where most (if not all) mods will be placed, depending on their next sub-directory.