Yeah, Ecobee (alone) can't equal out the temperatures in a house. But at least it gives you some ability to control the temperature of occupied rooms without having to constantly run back and forth to the thermostat.
There are two startup companies making "smart" air registers. IIRC, one company has said they will work with Ecobee. That would actually help control which rooms get the air when the HVAC runs, which could help equal out the temperatures. But it'll be first-gen, so who knows.
Which brand is the one that works w/Ecobee?!