Can batteries connected in series be treated as separate voltage sources?
In your first diagram the Zener is backwards and is just a diode shorting out the 5 V module. R will run very hot. It would be very unusual not to have common negative instead of common positive.
In your second diagram the batteries will discharge at different rates so it's not a good scheme. A low drop-out voltage regulator for the 5 V circuit would be a much better idea and improve battery life. (The Zener regulator would be conducting all the time and wasting battery energy.)