Leaving water out all the time for the puppies is perfectly fine and the puppies will then drink the water as they get thirsty and need a drink.
However if the puppies are not potty trained and are prone to go pee in the house at night then put the water up during the night so that the puppies won't get their bladder too full and pee in the house.
During the day when you're around you should leave the water bowl full of water out for the puppies to drink when they need a drink.
During the potty training of the dog be consistent with removing the bowl of water at the same time each night so the puppies will get used to it.
Let the puppy have the desired water throughout the day even when potty training them but at night remove the water bowl and when the puppy is potty trained and can hold it then it's okay to leave the water bowl out overnight for the puppy to drink from when it pleases.