Rain water shouldn't hurt any more than condensation in the pipes. If you want to drill a small hole to allow water to drip out, thats fine. Just be sure to touch the area up with some sort heat paint, to keep the exposed metal from rusting any quicker. We do not put a drain hole in the exhaust systems because we've found out that most people drive the truck daily, and what little water gets in, will be evaporated quickly. I've seen everything from coffee cans, to kittie litter buckets, to 1 gallon freezer bags being used to keep water our over night. The fun part about that is start up, and see how high you can shoot them puppies up in the air...LOL I think if you'd have an old soft cover for a truck bed, use that material, and make your self some outta that. Thats probably what I'll do once I get a truck to put stacks on it...LOL