I will try to split your requirement into two sub features and elaborate more on them.
First, you can draw shapes on top of all other shapes with Diagram Drawing tools
. To manually position shapes on top of other shapes you can set their ZIndex property. When you draw a shape , its Geometry property contains the drawn geometry path. Also, the Zoom and Pan operations will scale / move the shapes out of the box and you won't need to use separate canvas with lots of synchronizing code between the diagram and the Canvas.
Second, the animating of shape (path) moving along other shape (path) is a general well known problem in WPF and some approach can be used from forums / blog posts / codeplex.
We hope this helps.
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