No they don't come on deck but just sit horizontally at the level of the toerail outside the stanchions.
Works well unless you are very hard pressed with gunnels under. In which case I would remove and stow them.
Fenders will hardly help if another boat collides with yours when the wind picks up at night. What helps (talking form experience) is a large heavy anchor and long chain, so you can safely anchor away form the crowd.