I wouldn't put it on until a few layers after the first layer depending on layer height. To turn it on, the easiest way to do it is to manual enter M106 into your gcode after a certain layer to find the certain layer search for Z0.9 in the gcode file. There is also a cool plugin someone made that turns the fan on at different speeds throughotu the print when there are bridges etc.
Ryanmark is right. Somewhere in this forum, somebody implemented a replacement for the cool plugin that allows for better control over the fan. Look/search the skeinforge forum in the software section. I think you'll find it there.
