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Hens will lay where they want, but you can influence them. They like to lay in dark places, so put sides and a top and put the nesting boxes in the darker area of the coop. You might try moving the nesting boxes away from the wall and put the entrance on the wall side to make it darker. Or you could partially close in the open side to make it darker. I'd think a 9" square opening would be big enough for your hens to get into the nest. Someone with more experience might want to comment on the entry size.
A lip on the opening, probably 4" to 6" high, would make it harder for them to kick out the nesting material. A top on the nesting boxes will make it darker and keep them from perching over the nest and fouling it. If you make the nesting boxes dark or configured where you cannot see where you are putting your hand when gathering the eggs, I'd make the top hinged so I could open it to see where I am putting my hands. Black snakes especially love eggs and the older I get the less I like surprises.
To show them where to lay, put an egg or two in the nest. This could be a fake egg, like a smooth rock the right size or plastic Easter eggs. You could use a real egg, but I'd mark it with a soft-leaded pencil so I would know which one is not fresh.
The experts say you need one nesting box for every 4 hens but I'd be happy with two for 9 hens.
If you have roosts higher than the nesting boxes, they won't roost as much over the nesting boxes, but I would not expect them to completely stop perching there and fouling the nests.