I am about to cure that problem with my own house, it in my case needs the adding of a relay. However the house was when we bought it in a right state as far as central heating control went.
In my case there were two independent pumps, one for flat and one for main house, plus thermosyphon for domestic hot water. It did not work as if just one pump was used it would cause a reverse flow on the other system, there were a few ways to cure it, one was non return valves, the other was motorised valves, I selected the latter, however it left a problem. If I want to ensure the pump only runs when the valve is open then using the micro switch for that, so there was no micro switch available to run the boiler, so I intend to fit a relay.
I would have preferred one pump and two valves, but the plumber wanted to retain the two pumps.
It took a combined effort between myself and the plumber to work out what I had, there were isolation valves on the pumps, so the test was to turn off the valve to prove putting a motorised valve would work, as near impossible to trace pipework, it was the problem with control which forced me to learn about central heating.
Be it an annex or just up and down stairs there are three ways to get independent control.
1) Twin pumps. (Would need non return valves)
2) Twin motorised valves.
3) Using the thermostatic radiator valve (TRV) heads.
So already talked about twin pumps and motorised valves, so the easy method may be to use the existing TRV so if we consider one large system covering house and annex then you would need two on/off wall thermostats or timers wired in parallel so either can cause the boiler to run. The TRV heads can be replaced with electronic heads which can then be set to stop either the main house or annex radiators getting hot, best would be the TRV heads linked to thermostat, but it could be done without.
I fitted eqiva eQ-3 bluetooth heads to some of my radiators, although I did not want the feature, I noted when setting up you can link the heads so they work as groups, so one group could be annex, and other group the main house. At £15 each that's the cheap way, but reading through the reports Drayton Wiser, and Hive both do a system where the TRV head tells the thermostat when to call for heat, as does Tado and Evohome, I have Nest which works with Energenie TRV heads, I have had problems getting the heads to follow the thermostat.
So I am sure it can be done, however first you have to work out what you already have, and then you need to decide which system to go for, it does seem that EvoHome gets very few complaints and has been out for a long time, but the rest is seems like sticking a pin in when blind folded as there seems to be complaints about most of the systems, and I personally feel I wasted my money on Energenie and that eqiva eQ-3 bluetooth would have done same job for a 1/3 or less of the price.