There are a number of different ways to accomplish this. Some Mercruiser engines have an “Easy Drain” system. It is best if you consult your owner’s manual for instructions specific to your engine in this case.
If you have conventional drain plugs the process is straight forward. There are plugs in the following locations –
Loosen or remove the plugs (depends on type of fitting). You need to check and make sure water actually comes out. It is common for the opening to be plugged with sand or corrosion. Remove the plug completely and use a short piece of wire to clear out if needed. If you are going to add antifreeze (see next paragraph) replace the plugs at this time. If not put them someplace safe and install in the spring.
An alternative or belt and suspenders method is to fill the engine with non-toxic antifreeze. This also helps minimize corrosion of the inside of the water jackets. We like to drain the engine regardless as this minimizes dilution of the antifreeze you are going to add and eliminates the need to have the engine running. Once the engine is drained and the plugs are replaced find the hose that comes from the sea water pump (or from the sterndrive if you have an Alpha). Disconnect the hose from the thermostat housing and connect a piece of hose (usually 1 ¼ inch id) to the thermostat housing. It should be long enough so you can put a funnel in the other end and be higher than the highest point on your engine. Slowly pour non-toxic antifreeze into the funnel until antifreeze starts coming out of the exhaust. This is going to take about 2 gallons, maybe more.
PLEASE NOTE – this will do nothing for the oil, power steering cooler, etc – they must still be drained. As most impellers will swell from the antifreeze this will leave your impeller out of the circuit even though it should be changed in the spring. If you are not concerned about the impeller replace the drain plugs in your coolers. Put your funnel in the hose that you took off the T stat housing and slowly fill with antifreeze allowing trapped air to exit.