Eric - being in Pennsylvania, freezing weather and snow are an issue for you. Regardless of the type of cover, water will get into the boat and work its way to the lowest point (i.e., the bilge aka bottom of the hull).
During the warm weather, your boat is fine in the preferred spot although you may get some mold/mildew from any water remaining in the bilge. During the winter, find another spot where both the boat and lower unit has no chance of accumulating water. As Toxic noted, freezing water does bad stuff! Granted, you'll need a LOT of water to fill up the boat to get where the pumps, etc. are, but is it worth it to test out how much? Not only that, but the extra water weight that will accumulate is not good for the trailer either!
BTW - if you have a speedo and water pressure gauge on your dash, probably worth disconnecting those underneath the dash before winter as well. Even a small amount of left over water in those gauges can freeze and break the internals. Small step to avoid a costly replacement come spring.
