I'm not familiar with your computerized setup but burner can do it all without electric elements so if burner alone is not heating furnaces or water something else is wrong. Do you enable zones by any chance? Also, something that took me far too long to discover is on my dash is a switch for the furnace fan off, low, high. Without this fan enabled the very front will not heat sufficiently. So I suggest check your zone settings on the t-stat and also ensure fans are running as expected.