When radio navigating I mark DME to a know beacon (preferably the one I'm tracking). It's nice to be in the air overhead a landmark and have the expected DME reading on the box. I'll also add DME marks on my course for the boundaries of CAS (when applicable), my destination and any turning points.
Since the DME is not always at the station I'm tracking, I always mark the name of the DME with the d reading. So for example, tracking LIC to WPL NDB's I used SWB DME and mark the course with, for example, "06dSWB".
Also for VOR tracking I'll write the radial or reciprocal radial I intend to track on the map. (I.e. what I'll set the OBS to).
Marking wise - OHP permanent marker and a quick spray of Lynx deodorant. Care required with girlies in the plane - it's the Lynx effect.
(they just can't keep their hands off my map).