My experience is that the answer depends on what voltage your Kabola operates on. Initially, mine was 24 vdc, then had to be converted to 240 vac since the DC boards don't last with the voltage variations on a boat. When the controls were 24 vdc, the boiler would fire to maintain temperature in the water jacket. Once converted to 240 vac, it fires only when a zone calls for heat. I prefer the latter. If I understand your current setup, plumbing the heat exchanger back in series certainly makes sense, regardless of how the controller works, since engine heat does the work when underway, for free. If no zone is calling for heat, the circ pump isn't going to run, so you would rely on convection circulation, which I believe will work. In fact, stopping convection circulation prompted me to install electric ball valves in front of each zone loop which open when that zone calls for heat, which is what I did when installing warm floors in greenhouses. Without that positive shut off, hot water would always be slowly circulating.
There may be better ways of plumbing these systems, but mine works like this: Hot water exits the boiler and passes through a circulation loop on the hot water heater, then to the heat exchanger on the engine, then to water/air exchangers in each zone. I could have installed a parallel circuit from the boiler to the exchanger and back to heat water in the water heater that bypasses the zones when the engine was running, but why bother? Easy enough to turn the hot water heater on and use 120 vac to heat water even when no zone is calling for heat, a.k.a. summertime. Seems simpler to me.
If the heater is powered by electricity, it uses a thermostat to heat the coils. You can put another thermostat on the water heater is you want to, so the boiler will fire when it calls for heat. But then you need a bypass loop from the water heater back to the boiler, and you're using a 40k Btu boiler to provide 5k Btu worth of heating. So, in summer, I just heat the water using 120 vac since after all, it is a water heater. Hope that helps.