I went out to my garage the other day and was messing around with the aplha I drive on my boat. The temp was below freezing and I noticed a crunching noise coming from the drive shaft bellow as I moved the drive from left to right. I guess a little water had frozen in between the bellow pleats. I checked the bellow and didn't see any cracks or tears in it at all. How did water get in the bellow? I did wash out the engine compartment before I winterized the boat, could some water have gotten in that way?

The input shaft goes through a hole into the engine compartment. There is a seal but it's not real effective at keeping water out of the bellows from inside the boat. If it's cold enough for ice, you probably should not be turning the drive as it could damage the bellows. It's a good idea to remove the drive after winterizing to grease the u-joints. Stuff a rag into the hole in the bell housing and put an inexpensive plastic cover over it, and store the drive where it's less likely to disappear. Also recomended is drain and refill the drive after winterizing.
Last but not least, if you have ANY doubts as to the condition of the bellows, replace it. Do the shift cable boot while your at it.

yeah it should be two o-rings around the shaft..