One Furnace, Dual Zones -- Install Sensi on each?
The most common way that two thermostats work with one HVAC system is through the use of a zone controller like one of these.  They can be installed near the air handler, but it could also be in a nearby closet so it can be monitored or adjusted without going in the attic.

The zone controller makes all the decisions about controlling dampers and calling for heat or cool, so the thermostats don't have to know they are not controlling their own independent system.  The thermostats are "standard" and don't need any extra features or wire connections, so you should be able to easily replace them with a smart thermostat and follow the normal installation instructions.

You can verify this by finding the zone controller, or just look at the wiring on your current thermostats.  If they have the typical R, G, Y, W, C wires and nothing extra then its a safe bet they are standard thermostats.  If they have some additional wires (and you don't have a heat pump or multistage heat/cool) then it might take some more research.  Also look up the model numbers of the current thermostats.