If I put paper next to her bed, in the crate, Im telling her its ok to poo over night, which is what I want to discourage. Moving the paper closer to the door and then outside, is ok for during the day, but I can't leave the door open at night.

What you refer to as the yard, is in fact grass, so its not a question of being able to hose it down. Ideally it would be great if both the dogs would do it round the back of the flowerbeds, rather than all over the grass.

She feeds around 9 am and then at 5 pm. If I give her the second feed later, do you think the poo that is coming out during the night will not be due until the following morning?? What would be the maximum hour that a puppy should feed at night?