If you need free movable/draggable items you probably need a degree of flexibility that built-in controls don't really provide. You're better off constructing your own controls, perhaps deriving from existing controls that provide close-enough functionality.
So for starters you'd have a control for a box item and a control for an arrow. The controls need to be movable and draggable inside a container, so you'll also need a container, probably derived from Canvas.
What I'd really recommend is to have a look at Model-View-ViewModel techniques; they can be daunting for a beginner but the benefits are immense. In this case, you'd have a collection of objects that represent your structure; all the objects will have, for starters, X and Y properties that define their coordinates. The objects are represented on the page by the previously mentioned controls, with bindings from their relevant properties to the properties of the objects. The objects are the ViewModel, and the controls represent the View.
Then, when you move the items with the mouse (the code for that is pretty easy), the properties of both the controls and the objects are automatically updated. More properties for the objects can include size, labels, and a collection of snap points that represent where arrows can connect to the object.
Arrows can be represented with the same concepts, except that instead of explicit X and Y coordinates they would have associated objects and snap points; then their coordinates would be automatically calculated based on the positions of the snap points.
Based on these structures, you can do actions exclusively from the ViewModel, like adding new items automatically connected to their parents, and have the view update based on that.
This is quite a broad topic so I really should stop now; I don't even what articles to recommend to get you started. Probably anything by Josh Smith on the topic of MVVM :P