Well, its hard to argue with the results Billn mentions but here is how i do it...
I go two ways, first is pencil. I write on there then burn it in with a soldering iron.
Second is I sand the wood smooth then write in fine point sharpie. then seal over it with a thin coat of superglue after the ink has dried. Careful or the glue will smear the ink. After that has dried, you are good to put whatever you want over it.
Dont discount charcoal or pencil though. As a portrait and landscape artist, I often deal with these medium. Once done, I will take hair spray over the work to set the graphite or charcoal in. After that it can be handled without smudging. Perhaps the same concept but use something other than hairspray, like a watertight adhesive, I seem to recall buying some in a spray can for sealing wood at Walmart.