Q: Why do the plugins not show up?
A: This is related to a new Windows security feature.
The menu in the top right of the Explorer should have four buttons: "Plugins", "Preview", "Mod Manager", and "About". However, on first downloading and opening the tools, you may not see "Plugins" (see image below).
To solve the problem, you'll need to unblock a number of .dll files included with the Explorer. Head to MEAExplorerWV -> Release -> plugins. There will be a number of folders in that directory. Click on the first one, and you ought to see at least one .dll file. Right-click on it and choose "Properties" from the menu that shows up. In the window that pops up, select "Unblock". Repeat this process for every .dll file in every folder contained in the "plugins" directory.
When you launch the Explorer again, "Plugins" should be available.