UIManager can install mods directly from ZIP files. It can even install a number of mods contained in the one ZIP, as is common with UI mod packages such as Cosmos. The directory structure of the ZIP is irrelevant -- UIManager will automatically detect where the TOC files are in the ZIP and show you which mods you can install.
You can also use this program to change the TOC version to whatever you need. ie if the old version of your addons was 4449 and the patch changed to 1500, you can change all your addons at the same time to 1500.)
