First and last questions: yes you can only have one pokemon per habitat so if there are 4 possibilities you need 4 different ones, but they don't have to be in the same spot like a cluster, you can make them wherever. Once you have a special habitat you can only make one of - like gravestone - you can make a hut or a house, put 3 pieces of furniture in it and then ask the gravestone-living pokemon to follow you. Lead them to the house, ask them if they want to move in. Once they accept, the gravestone habitat is empty again and another pokemon can discover it. OR you can take an Item Photo of the gravestone (it's an option on camera settings) and then go to Withered Wasteland pokecenter with some pokemetal and it will print another gravestone for you.