Click on a tab, or drag an item from the Finder or a dock onto a tab to cause that layer to be brought to the front. You can add and remove layers using the menu items in the Edit menu, and show the layer tabs from the Dock Options window.
If you click on an item in one layer, you can drag it up onto another layer's folder tab which will cause the dock to switch to that layer, and then drag it down onto an empty space in the new layer. If you let go of an item on top of a folder tab, it will put the item in the first available free space in that layer of the dock if possible.
To rearrange the tabs, hold down Option and click and drag the tab to the required position (including into another dock). If you drag a tab to the Finder, the layer will be exported as a folder of aliases (or an HTML file in the case of a layer of URLs). If you drag a tab to the Trash, it will be removed.
You can also hide the title bar of a dock, so that the window shapes itself around the tabs. This frees up quite a bit of desktop space. To do this, uncheck the box marked "Show window titlebar" in the Dock Options window.
When the titlebar is hidden, you can drag around the dock window by holding down the option key and clicking and dragging in an empty area of the dock.
The cursor will change to a small hand to show you when it will drag the window.