I have tried it by just inverting the pen that I created, but you will have to be very careful to keep both ends parallel to each other with respect to the wii remote to make sure that the end that touches your surface is totally aligned to the other end where the IR LED is.  You will definitely benefit from the IR remote always seeing your IR source, but it would be a bit of a challenge if you would want to use your IR pen as you would do a standard marker/ballpen.  Ex. if I am going to write a down stroke onto the surface, the effect on the other tip would be an upward stroke as seen by the wii remote, except of course you keep the discipline of aligning both ends with respect to the remote mentioned earlier. 

and oh, I failed to mention.  If your pen is too short, you will not suffer from the problem that I mentioned, and tracking would get more accurate.  Depending on how you would want to write onto your board, I guess your setup is fine.  Some people prefer the feel of a longer pen, I know I do. 

Tracking works perfectly for me and mine faces the board. What is your setup of wiimote relative to writing surface etc..?

I  read this post the other day and it got me thinking. On my drive home today I came up with a concept and tonight I finished making it. I used an old glove. I cut off everything but the index finger and wrist band part. I attached the IR light to the back of my finger and the momentary button to the front of my finger. I ran the wires down the glove and hid the battery pack inside the wrist band. Now I have a pressure button pen that's on my finger. I tried it tonight in my classroom and it works very well. Plus because of the switch on the front, I know where I have to hit everytime to get what I want. It looks a little ghetto with my duct tape, but it's pretty awesome anyway. I'll put some pics up tomorrow after I use it with the students.

Congrats. I ahve the same idea, but with a wireless mouse on my wrist and a wireless IR pen with left and right click.