It appears that there is some confusion with the latest version. The documentation has been updated to reflect all the new features in V2.0+, and this is available in the "Description" section of
www.amiupdate.net.
The main cause of confusion here seems to stem from the fact that users have an icon in the AmiDock bar to launch AmiUpdate, and then having the "Docky" option set in the preferences means there are actually two icons showing.
The second icon is an actual docky. This has a context menu, which you can access by left clicking once on the docky, then right clicking while over it. From here you can carry out the most common tasks, including opening the preferences editor. If you want to show the interface, simply select the "UnIconify" menu item, or double-click the docky.
The docky will be animated when AmiUpdate is busy scanning or updating, during this time only an "Abort" menu item is available.
Please refer to the documentation
here if you require any more information.
Simon