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For what it's worth, here is how I changed the coolant:

I drained the coolant using the valve and drain hose on the port side of the engine. I had to remove the filler cap to get good flow. This allowed me to drain about 2/3 of the coolant. I then removed one of the hoses from the hot water heater. The heater and hoses hold a lot of coolant. I don't remember the exact amount but I think it was a quart or two. This is a good number to know, because the Yanmar manual will only tell you the coolant capacity of the engine. The additional fluid in the heater must be accounted for in order to get the correct anti-freeze/water mixture ratio. At this point I have drained most of the coolant from the system, but there is still some in the water pump and remaining hoses. After draining, I put the hose back on the heater and filled the system with DI water and ran the engine until the thermostat opened. This will flush the rest of the system. I drained the system again from the engine drain valve. I repeated the last few steps until I had (nearly) clear water exiting the engine. The cooling system is now filled with clean DI water. Finally drain enough water from the engine so the correct amount of antifreeze can be added, then run the engine to mix it all up. Keep an eye on the coolant level the next few times you run the engine. As Gerry pointed out air trapped in the system can suck the reservoir dry.

As far as choice of antifreeze, I was told not to use ethylene glycol based antifreeze because the antifreeze runs through a heat exchanger in the hot water heater. If a leak develops in the heat exchanger poisonous ethylene glycol can contaminate your drinking water system.

Kevin Thomas
#509/2-cabin, Marina Del Rey, CA