It sounds like you've received some good advice
As far as nighttime is concerned, I don't see any reason why you need to pick up the food and water. You can make it available for your puppy at all times. I know whenever I used to feed Miko dog food, I used to leave it down for him all the time. Sometimes, he would get hungry in the middle of the night, so I always left food out for him.
Also, I feel like water should always be available for them.