I don't know if you still need an answer to this or not, but I needed it as well and couldn't really find a good answer anywhere so I'm provding it here. You need to create a LayoutArchorable, set its Content to your UserControl, and then call the AddToLayout method on the LayoutArchorable to get it to add itself. In my case I wanted the new window to start as Floating so the user could decide where to drop it, but you still have to assign it somewhere before it can float.
LayoutAnchorable la = new LayoutAnchorable { Title = "New Window", FloatingHeight = 400, FloatingWidth = 500, Content = new YourUserControl() };
la.AddToLayout(dockingManager, AnchorableShowStrategy.Right);
la.Float();
In this example, I named the DockingManager in the XAML so I could access it from the code behind.