There are several ways to do this. The easiest way with the current release is to look in the org.activiti.designer.eclipse.editor.ActivitiDiagramEditor.doSaveToBpmn(Bpmn2MemoryModel, String) method. There you can see that a BpmnXMLConverter is created, that is used to transform the Bpmn2MemoryModel to XML. If you change the logic in there, you can output whatever you want once the model gets marshalled to XML.
Another option is to create your own ExportMarshaller. This is currently a disabled feature, but you can easily re-enable it by invoking your marshaller in org.activiti.designer.eclipse.editor.ActivitiDiagramEditor too. Or, you can wait for the next release, in which I hope to have the ExportMarshaller functionality back in there to use without changes.
Writing a custom marshaller can be quite a bit of work, though, so I'd take a look at changing or subclassing the default behavior from the first option I mentioned. That way you get all the default stuff, plus your extra XML.