Susan I just use a regular #2 pencil to write with.
Some of the paper clips do fade some but not too bad. I did use the wire that is for marking crosses as well but in these faded too much such as the purple faded to blue which was the exact color as the blue wire, the pink fades to white, and some others fade also. It wouldn't matter as long as you didn't use the colors that the others faded to. I threw away a whole lot of pods because I had no clue if the wire was supposed to be blue or if it was purple that faded to blue not to mention I had used wires that were blue and purple striped so I couldn't be sure what was what.