You need a 3-zone controller, and may not have it. Think of the water heater as a separate zone. It is often set up as a priority zone which means that the house heat won't come on if the WH needs heat. There are add-on controllers that could be used which would allow three separate thermostats to control the three pumps. www.taco-hvac.com has one that would work as seen in this catalog http://www.taco-hvac.com/uploads/Fil...ry/100-5.0.pdf. That's what I have in my house. One zone for the indirect, one for the radiant heat, and one for the air handler. Some boilers can do this with their existing controller, or may support an add-in board. If it can't, then the Taco unit, or one like it, would work.