In order to change his poop schedule you will need to change his feeding schedule. I personally believe that he will eventually be able to hold it all night. Meanwhile, I would give him a big enough area to accomodate a pee pad for him to use in the night.
My puppies are in a 4x4 x pen with a pee pad at pne end. they use that in the night.
here is a picture of my puppy pen.
IMG_1600 (750 x 562).jpg