Sounds like you have a good handle on it.
I wired my system with the breaker as my heat on off switch.
Off the switch leg I ran 3 wires.
#1 to the diesel boiler energize lead. (not main power lead)
#2 to the bedroom thermostat, and through tstat on to the hydronic fan coil.
#3 went to the living area thermostat and toe kick.
Wired this way when we need heat we turn the heat switch on and the boiler heats the system, and the tstats maintain the temps in the seperate areas.†
The boiler will cycle on and off as needed to maintain heat within the system.
Yes you can use† diodes so you do not energise all circuits at once.† :-\But as you mentioned just by running the boiler and circulating the hot water helps take the chill off and the toe kick fans realy boost the heat when you need it. I always turn the heat off when not needed anyway, so I didn't use diodes.
I also added potable hot water and baseboard heat with a couple of circulation pumps controlled by the tstats also, much more even heat and added convenience.
Put the boiler in the wet bay
If I had heard one run I would not have put mine in the engine bay, and the heat in the wet bay is a bonus.
Good luck with your choices.