I haven't used Homekit, so I can't speak to that, but I have had an ecobee for several years now, and it's integrated into HA.

It's not clear to me if your setup is "1 heating system for one room, and a second system for a different room", or if it's two heating systems for the same area.

In the first case, I don't think it'll work - ecobee is only designed to control one heating system. The remote thermometers just tell it what's going on where they are, so it knows if that room needs more heating or cooling. If they do, then it fires up the HVAC to make that happen. You can tell ecobee which thermometer(s) to use to trigger the HVAC - at night, you probably care about the bedroom more than anything else, while in the day you probably care about the living room more. But it can't simultaneously control two separate systems.

If it's the second case, ecobee does, I think, have provisions for two stages of heat, so it's possible you could set it up to use the second HVAC as stage 2. But I'm not certain about this at all. You might need an additional relay, I'm not sure.

But I think there might be an easier solution that doesn't require a full blown second thermostat using HA, and this is what I do for our pellet stove (we have a main household HVAC, and a pellet stove for extra heat). Get something like a Shelly 1 and use that to trigger the second heat system. Then put in a temperature sensor - an ecobee remote sensor, bluetooth, wifi, Zigbee, etc., whatever works best for you - and with those two things, you can create a "thermostat" entity in HA, then use a thermostat card to control it. Assuming HA is running and it's getting info from the thermometer, it works well. Of course you'd mostly access it on a phone or computer, not something mounted on the wall (unless you put a tablet on the wall to view and control HA, but that's a whole different project).

This isn't necessary for it to work, but I have a script set up that has logic such as: []If the outside temperature is above 50 degrees, set the thermostat to 50 so the pellet stove shuts down and doesn't restart. (Don't need it.) []If the outside temperature is below 45 degrees, set the thermostat according to the rules below. []At night set it to 70 degrees, during the day, 72.
[]If the outside temperature is below 32 degrees, set the thermostat to 78 degrees so the pellet stove stays running.