It's nice that you want to let them have their space. But, keep in mind that cottonmouths are very territorial and aggressive. If you know you are sharing a home with one or more, be very aware that you should not venture into the snake's territory. Snakes do not consider any of the property yours, and cottonmouths will aggressively strike and try to remove you from their homes. I have worked with and around them for many years, and I leave the ones in the swamps and wetlands alone when I venture into their homes, but we do kill the ones that try to move in to our home/yard. I am very tolerant of snakes and wildlife, but aggressive poisonous snakes are dangerous, and a bite can kill a small child or pet very quicklly... a risk I'm not willing to take with my children.
The alligator can stay around as long as he continues to stay in his own yard and remains afraid of people, but we will have him moved if he starts hanging out in our yard looking to be fed.
Good luck with your resident cottonmouth. Hope no one gets bitten! With any luck, he was just passing through your yard, and not considering moving in. If you have a pond, wetland, or other permanent water body on your property, be careful around it.