The relay is a band-aid fix. The chimney should be large enough to handle both appliances at the same time. It may be that the burner nozzle is too large, making the combined fires too much for the chimney. The relay would let the larger appliance fire and perhaps force the gases backwards into the water heater, making soot there.
The National Fire Protection Association has books for chimney sizes according to the combined inputs of appliances, the chart may be in the instructions that came with the appliance. An experienced plumber can follow these directions. In any case, find an experienced burner technician to set up your fires safely.