There is only one a/c compressor, but there are two evaporator, front and rear. There are also two HVAC (heating ventilation air conditioning) fans, front and rear. There are also two seperate HVAC controls, front and rear. If you set them both to AUTO, they will do just like Flint said, front and rear fans will adjust their speed, temp sensor will add/decrease heat as needed, each intedenpant of one another.
The a/c compressor is going to run as long as the a/c is on no matter what you do.
There is no added strain on anything, the a/c compressor only knows on or off.
If you turn the front HVAC off the rear will still operate. Turn the rear off and the front will still operate.
It's like the a/c in your house, you set the temp on the thermostat and it does the rest, same thing on your truck.
I leave mine set on AUTO, both front and rear, all the time, winter, summer, doesnt matter. Let it do it's thing.
The only time I change it is if the windshield is covered in ice and needs to be cleared, then I put it in defrost. Built go back to AUTO once the windshield is cleared.