I am afraid, I do not understand what you are trying to achieve.
You are trying to create a specific type of diagram in yEd, right?
If so, can you post an illustration of an example (e.g. from a different application or a mockup created with an image editor application) of the desired diagram type?
If not, which yWorks product are you using?
Let me rephrase my question. What do you mean by "annotations to nodes"?
In yEd, the only thing called "annotation" is the BPMN annotation symbol
Are you actually asking about labels (i.e. adding text to nodes)? If so, labels for edges are already supported. (Select an edge, right-click the edge to open its context menu, and choose "Add Label".)