House training a puppy is a relatively straightforward process. It does require patience but there is no great mystery to it.

 
Puppies are constantly growing, eating varying amounts and developing in fits and starts. Most puppies aren’t fully capable of “holding out” consistently until they are around six months old.
Larger breeds sometimes take longer to house train due to the variance in muscle mass and growth rate. 
No matter what size or shape, the golden rule is to consistently present the puppy to his toilet place:

1. First thing in the morning
2. When he wakes from a nap
3, After he’s eaten
4, After he’s had a drink
5, Before he goes to bed.

Speak the words “be clean” as he eliminates and praise him afterwards.
Reward successful visits and ignore mistakes. Don’t resort to scolding when he has an accident in the house.

The key to house training is to set him up for success and be consistent. The more he is presented to the designated spot and eliminates, the quicker he will learn what is expected of him. If he realises that going to the toilet is a rewarding experience he will be happy to go to his area and eliminate on command.

Crate training is another technique used to toilet train puppies. Dogs do not like messing their beds. Confining a puppy in a crate for 30 minutes or so teaches him how to hold on and control his bladder. He’s usually ready to eliminate by the time he is released from the crate so this method helps him to understand what is expected of him. Be very careful not to leave him too long and let him mess or you’ll set things back.

I often use toilet training as an opportunity to start training the puppy to come when called (recall training). I clap my hands and say, “come, come” when he has finished eliminating.
The puppy normally feels better after he has relieved himself so an excitable, high-pitched vocalization or whistle is usually accepted with enthusiasm. The puppy normally responds by bounding toward me to get a nice treat and loads of praise. By doing this routine we are conditioning the puppy to return to us on command.

Dogs are generally clean animals and won’t mess their place if they can prevent it.
Problems with dogs messing the house can normally be attributed to inconsistent house training techniques, an irregular exercise schedule or dominant boundary marking. 

With the exception of boundary marking, a condition that can normally be cured by neutering, most toilet training issues can be resolved by monitoring food and liquid intake together along with regular exercise.

Take time to accustom him to his new schedule. I find stable, well-adjusted dogs wont mess indoors.
Patience and consistency is the key to successfully house training a puppy.

A word of warning; sometimes dogs develop bladder or bowel problems that prevent them “holding out” to their next toilet break. Please contact your vet if you continue to experience house-training issues.