On my boat there are two water loops to the heater, potable water and the heating loop from the engine.
Putting the non-toxic anti-freeze in the empty water tanks and getting flow from both hot and cold water sides of all fixtures and sucking the anti-freeze into the engine raw water loop to protect that heat exchanger and the muffler will protect the equipment in the boat
If the boat is hauled out the through-hull drains should be closed so that you can move the valve a bit and close so some anti-freeze is in it to protect it. I do this with my boat in the water.
I also have three drains on the water heater to drain it, but this would not protect the water lines.