Hiya and welcome to the best website in the world!! (No, I don't work for them but have just found them soo helpful being a newbie myself!!)
We have a coop with two nest boxes and four hens and my hens sleep and poop in there too, I just make sure they are cleaned out often. They also lay their eggs in the same place so if you are doing it wrong, well then so am I!!!
I know this isn't really very helpful but it is, when you know you are not alone!!
xxx