Watchtower main panel has 3 buttons. It is possible to align them vertically in settings.
Click it whenever you need to sync folders. If you turned on auto sync, you can forget about it :)
Opens a menu where you can add/remove watch folders from your project. Also you can adjust if folders should use image sequence import, be flattened or use relative path.
Select one bin in your project, alt+click on select folders button and you will be able to link folder to that bin.
In settings you can adjust import options, filter for file extensions and folder names, deactivate license on current machine and download update.