pyCloudy is an interface to Cloudy, it is used to generate the input files, run the code from within a python script and read the output files. You r question seems to me more about what can be done with Cloudy itself, rather than dealing with pyCloudy. I then recommend you to have a look at the different Cloudy manuals, starting with the Quick Start and eventually reading the Hazy (volume 1 and 2) to have an idea on how you can obtain the ionic fraction of the different elements, corresponding to the model you are interested with. Then you can come back to pyCloudy and play with the Cloudy outputs, including the ionic fractions, as described in this example perhaps:
https://sites.google.com/site/pycloudy/examples/example-1 .