Leave them in the folder they download to in usb helper and try to download it again. Usb helper will validate and verify the files automatically and if all is well, it will say your titles are ready.
If your botw game installed fine, start the game and make a quick save data file. Delete that games wup folder from your sd/install folder and then place the update file folder into sd/install so that is the only content in there.
As said earlier, they won't show if you have that folder in another folder within the sd/install. (you may not have done that but it is a simple mistake to make!)