Two heater/AC units and two thermostats

We're about to close escrow on a new house that has two forced-air heater/air conditioner units and two thermostats. I don't quite see how this is going to work.
One unit is for the master bedroom, guest room, and their bathrooms, I'm told, and the other unit is for the rest of the house (one story). The house is L-shaped, with the master bedroom, and one thermostat, at the end of one piece, and the guest bedroom at the end of the other piece. The thermostat for the rest of the house is right at the corner of the L.
Is this going to be comfortable? How do we set the thermostats up for this? I'm told we'll save money with the two-zone system, but I'm having trouble seeing how.
I assume I should start warming the bedrooms up from the night setback earlier than the rest of the house, to warm up the bathrooms and make it easier to get out of bed. And I can start the night setback earlier for the bedrooms, to start them cooling down for sleep.
What about running the two at different temperatures? The master bedroom has 8-foot double doors and the guest room has a regular-sized single door, so I think there won't be a lot of mixing. There are returns in both of the bedrooms, too. The returns for the rest of the house are nearer to the L, in the center of the house.
Mary
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Mary Shafer Retired aerospace research engineer
snipped-for-privacy@qnet.com
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