The wires connect severs and switches, not the racks, right? Model the racks as table nodes. Model your servers and switches as normal nodes that are child nodes of the rack table nodes.
Sample GraphML.
If the table is empty after a layout calculation, the server and switch nodes were not properly assigned as child nodes of the rack table node.
Try layouting the sample graph in my answer (using "Layout" -> "Swimlane" -> Hierarchic"), both the server as well as the switch node will stay inside the rack table node.
Please see chapter Grouping Support in the yEd Manual for more information on nesting nodes.