If you want to raise a puppy that is calm, confident and reliable, then teach him boundaries and be consistent in enforcing them.
Establish your House Rules.
Puppies are like toddlers. They need constant supervision. They need a schedule so that they can learn to understand and meet your expectations. They will understand what you expect if you are predictable. Be consistent with a puppy and he will happily do what you want.
Because you can't supervise your puppy 24/7, you have to teach him to accept limits to his freedom and confinement in a safe area where he can relax and sleep. Allowing a puppy free access to the entire house is not a good idea. Puppies have to earn their freedoms gradually over time.
A puppy that learns to accept confinement and understand that it is OK to be alone for a little while will mature into a more confident adult that understands and respects leadership. Whether you use a crate or a small gated area to confine your puppy, time in his special place should be a normal part of his daily routine. Viewing confinement as a way to react to undesirable behavior (chewing, house soiling, etc.) is not a proper use of boundaries.
If you make confinement a punishment, you are sacrificing a valuable training tool for raising a well adjusted puppy.
Alternate confinement with exercise (walks on leash, potty breaks) and supervised play time (indoor and outdoor games). Create a schedule that meets your needs as well as the needs of the growing puppy.
Raising a puppy takes time and commitment. There aren't any shortcuts. But the effort you spend in the puppy's first months will reward you with many years of joyful canine companionship.