Normally, water enters the muffler only via the engine's seawater cooling circuit. If you drain the muffler while in the water, and then use the engine to get over to the launch well for haul-out, you will get water in the muffler all over again. Drain it after haul-out to be sure.
Or... After haul-out, I jam a length of 1/2 inch OD clear plastic tubing into the seawater intake port from outside the boat. A little Vaseline helps it go in easier and seals against vacuum leaks. Then place the other end of the tube into jug of antifreeze. Check and double check that the transmission is in neutral gear and start the engine. The antifreeze will feed into the seawater cooling circuit and out the exhaust port. I feed one gallon of -50 to displace the water, and follow up with a gallon of -100 to displace the diluted -50. No need to drain the muffler because it will contain no water, only antifreeze. You can tie a bucket off the stern rail and position it to catch the antifreeze as it exits the exhaust port (let the initial flow of water bypass the bucket and catch mostly just the antifreeze), and then pump the bucket contents through the head to protect the holding tank. The same "tube in the intake port" trick can be used to pump a gallon of -50 through the head intake system. Just hold the "flush" button until the jug is empty. As a final step, I remove and drain the two intake strainers (one for the engine, the other for the head), and remove the impeller from the seawater cooling pump so that it won't marinate in antifreeze all winter.