How do I add a player to a faction? during a stage quest ...

If they should be in the faction for the duration of the quest you can simply add that faction to their alias. Otherwise you can use YourActor.AddToFaction(YourFaction) in a script.

no I wanted that the player can enter the ship without getting ganged up when the quest ( third one is started ) and how can I do also to allow him to sleep in a bed?

actually I want to trigger something liek this when the player goes to sleep ...

he goes to sleep and the next stage of quest starts , teleporting the whole ship in another space ( disabling enabling thing )

Make the player the owner of the bed

http://www.creationkit.com/AddToFaction_-_Actor
http://www.creationkit.com/RegisterForSleep_-_Form
http://www.creationkit.com/OnSleepStop_-_Form
http://www.creationkit.com/Reference#Enable_Parent