When training a new puppy you need to teach him to be submissive and recognize you as the leader of the pack however if the new pup is too submissive he will be to fearful of you to learn.
How do you help a submissive puppy overcome his shyness and build self confidence. There are several methods to help your new dog overcome his submissiveness.
Never pet, play with or caress your pet when he shows signs of distress, this will only reinforce his submissive feelings.
If the puppy shows signs of fear try to redirect his activity to something he enjoys like taking a walk or playing fetch however do not ever reinforce a behavior that you do not want to see repeated.
You should spend regular amounts of time grooming your puppy and complimenting him. Your dog will come to enjoy this time spent with you and that will help to form a very strong bond between the two of you.
Make sure to provide him with a favorite treat when the grooming session is over to further reinforce the activity.
Feed your dog at the same time that you eat. Once he builds up his confidence you will start having him eat after you as part of his obedience training.
You should designate a special chair for your puppy near where you sit. You can cover the chair with a towel or old sheet to protect it if need be. You could even keep a couple of his favorite toys in the chair. This gives your pet the idea that the chair is part of his territory.
The puppy needs as many new life experiences as possible so that he learns the two of you will be together and that you as his leader will insure his safety.
These are examples of things you can do to build trust between you and the puppy. In time this will increase your dogs self confidence.