Have a look at this file. It shows how to script an entire phyloGenerator with only a few lines of code, and show show phyloGenerator keeps track of things like genes and DNA sequences.
Have you put the phyloGenerator.py file on your os.path? Have you made sure the 'requires' folder is in your working directory? If so, contact me.
I'm really sorry! Please contact me with specific questions, I'm happy to help. I'm afraid this is a rather basic introduction, and assumes that you know some Python already. I'm hoping to put something a little more concrete together in the next few weeks - watch this space. Maybe sign up to the mailing list for more info.