It's quite straightforward to make the molecule in the old version and import it in the new, the syntax for the molecular setup is the same. So, build it in 2008.10, and then just move it over to 2009.12 for semi-empirical calculations, for instance.
The only thing you need to change in the script will be "from ATK.KohnSham import *" to "from NanoLanguage import *".