Units placed inside your bunker provide no defense, but they can not be destroyed by attacking forces.

You need to keep defensive units outside of your bunker in order to protect your base (lest another commander occupy it).  I WOULD keep your offensive units stored away in your bunker, however.  (They're trained to run, gun, and attack the enemy.  IOW, they're useless in a defensive situation.)

I would keep some defensive units inside your bunker as a reserve (in the event of an occupation attempt that wipes out your primary defensive forces).

I have try to find answer from field manual with out luck. I´m a newbie and wonder if its matter for defence is my units in bunker or not?

Commander..The bunker keeps your units from being destroyed..Offence should be kept in Bunker except when in use..Never leave the game if all of you Offense is not in bunker..Defense should also be kept in bunker unless you are defending your base or that of a friend or ally..Never use Offence for Defensive measures..and likewise,,,never use Defensive units for Offensive attacks...If you are attacked any units on your base that is not in bunker is subject to be killed