There is no dedicated documentation feature in yEd. However, you could add a description to each node for that purpose.
To do that in yEd, select a node, then scroll the properties view (in the lower right corner) down to property "Description" in section "Data" and add your documentation text in the corresponding text field. Alternatively, use F6 to open the properties dialog for a selected node, go to tab "Data" and enter the description in the corresponding text area.
To do that in GraphML, add an attribute with name="description" of type="string" and scope for="node" and for each node you want to document, add a corresponding <data><![CDATA[Your documentation here.]]></data>. (Try creating a graph with only one node in yEd, add a description in yEd, and finally save as GraphML to get an example.)