First I put out my desks how I want them. It's important for me to be able to hang out in the middle, a "runway" of sorts, and also to walk through to the back and around the back and sides without moving desks. This way I can use physical proximity whenever I need. and I don't want anyone to have to stare at the back of most of their classmates' heads. This setup works well for me.
Next I do a quick sketch of the room. When I'm satisfied with the sketch, I make copies. I do new seating charts every quarter.