I have a quite similar configuration. Thermostats + wall thermostats + window contact. I have coupled them via the CCU and also created a configuration with different time schedules on the CCU. This has the big advantage the everything works even if my openHAB system or the CCU is offline because the devices can communicate with each other.
In openHAB I have only configured the wall thermostat as a thing to check and manipulate the room temperature (even remote). I have some plans for specific rules but did not find the time yet. By only working with the wall thermostats It will be able to keep the rules as simpler (at least I hope so).
It is possible to switch between auto and manual operation within rules, but as far as I remember this is not very intuitive.
Maybe you can find some helpful information in these two posts
