This is do-able but some of the calculations will be hard-coded in your Grasshopper definition given how Honeybee legacy is set up right now.
First, I would note that it is relatively straightforward to set up a zone with both operable and fixed windows like so:
To set different windows with different fractionOfGlzAreaOperable, you will have to use multiple Set EP AirFlow components for each group of windows facing a given orientation. For each Set EP AirFlow component, you should use the 2 - CUSTOM WIND / STACK VENTILATION option and input the total area and total height of open windows for a given facade. If you need help calculating these values, you will see in the screenshot above that the readMe! output of the component tells you these variables when you use the 1 - WINDOW NATURAL VENTILATION option.
Here is an example of a script where I set the south window to be 50% operable and the east window to be 25% operable:
When we eventually add support for the airflow network in Honeybee[+], this process will become a lot more straightforward and you will be able to assign a fraction operable to individual window surfaces.