Our last house had an atrium that could be accessed through a sliding glass door. My wife said that she thought she saw a skunk in there, but I figured that it must be a neighborhood cat. One night my wife woke me up to check out munching sounds in the atrium. Sure enough, there was a skunk in there eating some plants. It turned out that the skunk was living under our house. We called animal control and they offered to bring out a trap. We asked what they would do with the skunk after they trapped it and the answer was that they would euthanize it. We decided to leave the skunk alone, and other than occasional munching sounds there were no problems. It sounds like you have a friendly skunk, and if you leave it alone then you may be able to coexist peacefully.