Steve, I use Faber-Castell artist India ink pens. It's India ink, but eliminates the ink wells and tips used with them... they work more like a Sharpie, but with infinitely better ink. They come in different nib sizes, and in fact, you can get a set of them in different sizes to see which you like best for less than $8 on the big auction site.
I write on raw wood, or wood that has been dyed, let the ink dry, hit it lightly with spray finish, let that dry for a bit, then commence with the spraying process. It would also work fine between coats if the one beneath it was dry... and perhaps that would be the better route to take if you thought you might not get it right the first time and had to wipe it off and start over. Of course, try it on a test piece with your choice of finish to make sure they're compatible.
India ink won't fade over time like some others... like Sharpies.
Another pen I've had really good results with is the Jelly Roll ball point pen... in black and silver. I treat them just like I do the Faber-Castell pens as far as the finish goes. I've found them at local craft supply stores. They too are hardy, come in many different colors, and have not faded over time.