Am I correct this is the 240EFI Sportjet by Mercury engine? All of the cooling water will run out of the engine so there's no danger of freeze damage. But you should peridically and especially for winter, perform some preventive maintenance.
If I have time and materials it's best to wash and wax the entire hull, inside and out clean the vinyl seats with vinyl cleaner or mild soap and water, then spray and wipe with 303 vinyl conditioner.
As for the engine, I would remove the spark plugs and squite each cylinder with fogging oil or 2-stroke non-synthetic, a shot about the size of a quarter will do, maybe 1~2 seconds from an areosol fogging oil. Then before reinstalling the spark plugs turn the motor over by hand preferably, to distribute the fogging oil. Don't use too much, just enough to coat the cylinder walls with a mist.
Hopefully you already put fuel stabilizer in the fuel tank for last outing, to get the stabilizer circulated throughout the fuel system. If not then put the stabilizer in and fill the fuel tank. Filling tank helps to avoid condensation and water trapped in the bottom of tank What does that boat hold, about 20 gallons of fuel?
Replace the spin on fuel filter either now, or in the spring (I prefer AFTER spring startup, but in any event pouring the contents into a glass jar allows you to inspect for water that might have accumulated. Water in your fuel system will cause corrosion thus it's undesirable. Many times water enters through the fuel filler if the rubber gasket or o-ring is missing or damaged. Anyway, check the spin-on fuel filter for water before winter layup and then again in spring. Some 2-stroke oil as lubricant on the gasket of the filter helps getting it on and off.
Spray over the engine to make a light coating of fogging or preservative oil, this will help to reduce external corrosion due to moisture in the bilge.
You may remove the battery and take it indoors for maintenance charging if you have a good quality battery maintainer or leave it in boat if there's a built in battery maintainer. I have a 12v accessory socket installed directly connected to the battery in my boat for this purpose, I plug the maintainer into this socket. This allows me to once a month plug it into AC and observe if the battery has discharged. Usually if the battery is in good condition, the charge light flips to green quickly within a minute, if it takes an hour or more to turn green (float mode) this raises a red flag.
You should also change the jet pump stator oil in case it has gotten water in it, and the jet pump gearbox oil should be checked for signs of water or changed if that wasn't done recently.
After 1st startup in spring, you should replce the spark plugs with new ones. The reason to do this AFTER 1st startup is the plugs will be coated with fogging oil during startup and might foul, so preferably replace them with new AFTER 1st spring startup.
For further info, here's a link to a previous discussion for what needs to be done for the Mercury Sportjet EFI
http://www.seadooforum.com/showthread.php?55882-Winterize-and-De-Winterize-2004-Islandia