Dear Marcus,
I haven't used the 'Automatic Installer' version, but I believe using it doesn't mean it forbids doing a manual installation of the parallel version afterwards. I assume that you have to skip the steps that have been done automatically, i.e. python installation, gfortran installation, PATH environmental variables etc.
If you want do do a parallel installation, I believe you need to install mpich2, download the pre-compiled METIS library and configure the systel.cfg file for a parallel configuration.
Try do follow the installation instructions with python on the website and also have a look at this thread:
Working parallel installation using python/gfortran in Windows
To do a manual installation requires a bit more effort but you get a much better insight.
I hope it helps,
Costas