To begin, purchase at least four litter boxes, remove the tops, fill them two thirds of the way full with litter, and place them in four different areas in your home. You want every section of your home to have a litter box that is close enough for your puppy to see or at least easily remember where it is. If you home is very large, it is best to focus on only one level of your home at a time and block off the other sections. If your home is carpeted, then you will need to block off the carpeted areas as much as possible until your puppy begins to prefer eliminating in the litter boxes.
Add scent to each litter box to encourage your puppy to eliminate there. To do this, you can purchase a spray from your local pet store designed to encourage your puppy to pee or poop, and spray the boxes at least three times a day. You can also add scent by placing one of your dog's poops in each litter box. When your puppy poops in the box, leave the fresh poop and clean up the old one each time. Always clean up pee.
Every two hours, encourage your puppy over to a litter box. Praise your puppy for sniffing, touching, or stepping into the box. If your puppy seems fearful of the box, then offer him a treat whenever he explores the box. Only offer a treat for exploring the box if you puppy is afraid though. If your puppy chooses to eliminate in the box after smelling it, then softly praise him, and when he finishes, offer him two treats, one at a time. Be careful to keep your voice soft and kind when you praise him, so that you do not distract him or scare him.
If your puppy does not eliminate in the litter box when you bring him there, supervise him in your home for the next thirty minutes. After thirty minutes, encourage him back over to the box. If you are using the spray and he seems distracted whenever he is in the litter box, then you can reapply the spray while he is still outside of the box. If he still will not go, then repeat this process every thirty minutes until he goes.
While your puppy is free, watch him carefully for signs that he is about to eliminate. This is especially important if it has been more than two hours since he last pooped or peed. Signs that your puppy needs to go can include: circling an area, sniffing the ground, squatting, lifting a leg, whining, pawing at you, barking at you, or trying to sneak away in order to eliminate out of your sight. If your puppy does any of those, quickly, but gently so as not to scare him, pick him up and carry him over to the litter box and place him inside it. If he eliminates there, praise him softly, and when he finishes offer him two treats, one at a time.
Continue to bring your puppy over to the litter box every two hours, until your puppy will occasionally go over to the box to eliminate on his own. If he goes on his own, follow him over quietly and reward him when he finishes. When your puppy begins to go on his own, then change the frequency of your trips taking him, from every two hours to every two and a half hours. If your puppy continues to be accident-free, and even increases the frequency of his trips to the box by himself, then increase the time between taking him to every three hours. If your puppy begins to have accidents at any point, then reduce the time between your trips by thirty minutes, until your puppy is making progress again.
When your puppy is consistently going to the bathroom on his own, then eliminate one of the litter boxes and space the other three slightly closer to where the removed box was. Choose the box that your puppy tends to go to the least. If your puppy does well going to the remaining boxes, then, after one month, remove another box, and space the remain two closer to where the removed box previously was. If your puppy does well going to the remaining two boxes without any accidents, then you can try removing the second box, so that there is only one box left. If your home is very large, then your puppy might need more than one box. If this is the case, then you will want to leave two litter boxes, with one litter box on each level or in each section of your home. That way your small dog does not have to go too far to find one.
If your home is large and you blocked off areas earlier, then you can now include those areas in your puppy's space if you wish for your puppy to go there. To do this, gradually add the space from those blocked areas back into the rest of your home, where your puppy has been spending his time. A good way to do this is to move a baby gate farther and farther into the blocked space. or to add one new room at a time, until you have eventually added all of the rooms that you wish for your puppy to go in. Make sure to keep this process gradual so that your puppy can practice going back to the litter box to eliminate from those new areas, and does not eliminate in the new space.