I have 5 WoW folders as well, but the Data folder is Symlinked in the 4 clone folders to the main install folder. This allows to have different settings for each instance, and increase performance not mention some extra drive space - each clone folder is about 20 MB.

For updating here is what I do:
1. Launch WoW from the main install folder. This is the one with the full Data folder. This patches the executable and data files. Quit after patching.
2. Copy all the files from the main WoW folder, but NOT the folders, into the clone install folders. You may also skip any of the specific patches and respective downloaders.
3. Launch keyclone and play