Timing, as they say, is everything. Little kids, as most of you know, wake up at the crack of dawn. So do young puppies. What's the first thing they need to do? You guessed it, they need to go to the bathroom. So unless you're one of those people that actually gets up at or before sunrise, the timing of when you feed your pup is important. When you are house-breaking a pup, you should set their mealtime for late in the morning and as late as possible in the evening. As they get older you won't have to do this, but with puppies, the later in the evening you feed them (and take up the water bowl) the easier it is to take them out first thing in the morning.
They will have fewer 5 AM accidents and you can take them out, and you should, as soon as you get up. If you feed them at 5 PM and let them drink all the water they want until 9 PM, you're really asking them not to poop for more than 12 to 14 HOURS and not to pee for more than 8 to 10 hours. Most pups just can't do that. It's physically impossible. Even if you take them out before you go to bed, which you should, you're still asking them to "hold it" for longer than they really can. Puppies have little bladders and as they grow their bladders grow and the muscle tone grows with it. Believe it or not, puppies do know they are not supposed to pee or poop in the house. Their mother begins housebreaking them within a few weeks of their birth. After she feeds, she will take the pups out of the lair, and let them do their business. Momma will clean up the lair so the pups know that their "home" is not to be used as a toilet. Your job is to continue what Momma dog has already started teaching her pups, you don't "go" in the house! Although they are probably are confused when you pee and poop in their "water bowl." (if you have a toilet bowl drinker)
Other than taking them out the moment you get up, the next thing you need to teach them is to "tell you" when they need to go out. Having a doggie door so they can go out whenever they need to or taking them out every two hours is NOT house breaking. A true house broken dog can tell you when they need to go out. You can start this by waiting for 15 - 20 minutes or so after they have eaten breakfast - and you know they have to go out again, stand by the door and ask "out?? They really do have to go, but you want them to respond to your question, "out?" the instant they bark, whine or scratch at the door - praise them profusely and take them out immediately. This way they know they have to "ask" to go out. Most pups can be almost completely housebroken in less than a week. Accidents will happen, for maybe a month, but no more than a month. If they keep having accidents after a month, chances are, you are doing something wrong. Remember, their Momma has already started their training, all you have to do is just finish the training!