If you on a trailer, Lower you engine so the water drains out of the foot cavity. If you will sleep better, throw a blanket over the engine cowling.... If its in the water, I would lower the engine also for the same reason, Thats all I've ever done and all I ever plan on doing minus the blanket also. I've had a bunch of inboard gas boats at my house and the engines were always fine down under the cover. I normally close all thru hulls, so thats not a problems.
Personally, I'd worry more about your pets....
Motors are easy- bigger problem some don't think about are the lines, check valves, and filters on the live wells and pumps inside the boat. One cracked or broken filter on your wash down or live well pump and next trip out you start taking on water!!!
One thing I've gotten into the habit of doing is trying to make sure most of the lines are dry at the end of my season, then I wait to have the annual service done at the beginning of the season before we take her out so the shop can check for any other leaks!
Had a friend of mine almost lose a boat because a hard freeze busted a pump screen filter- started taking on water faster than the bilge pump could keep up with it! http://www.pensacolafishingforum.com/f26/watch-those-lower-units-tonight-473841/