That is where they should lay eggs(the nests), not sleep....or you'll have poopy eggs.
Here's some great tips on how to modify that type of coop:
http://www.backyardchickens.com/t/1134399/help-hens-roosting-in-nest-boxes/10#post_17749535

Here's some great tips on how to modify that type of coop:
http://www.backyardchickens.com/t/1134399/help-hens-roosting-in-nest-boxes/10#post_17749535