@OP You should have a folder containing the main game and one for the update. And, optionally, 1 for the DLC
After decrypting them with CDecrypt, you'll get 3 folders for each: code, content, and meta.
Place all three of the folders for the main game wherever.
For the update, place all three in <cemu installation folder>/mlc01/usr/title/00050000/101C9X00/
For the dlc, place all three in <cemu installation folder>/mlc01/usr/title/00050000/101C9X00/aoc/
X varies by region, 4 for USA, 5 for EUR, not sure what Japan is.
I recommend you download the shader cache from /r/CEMUcaches. Use whichever has the highest shader count, I think it's 9800, and it'll take a long time to compile. Put your CEMU cache folder on a 700MB+ ramdisk for a massive speedboost.
Then, in CEMU, load the file <main game folder>/code/U-King.rpx
Note that BOTW is not currently possible to complete in CEMU. In fact, it's not even possible to get past the first shrine.