It can work both ways.
If you select multiple thermostats in a single instance of the app, then it applies the configured schedule to all the selected thermostats.
On the other hand, you can install the app separately for each thermostat and have independent schedules for each thermostat.
In exploring its full potential, taking it one step ahead, if configured correctly using Modes, you can even run it along side other thermostat apps like the Ultimate Modes Based Thermostat and Motion Sensor Based Thermostat on the same thermostat.