Possible Clues:

• Roof's perfect covering flat evenly
• Officer covered by transparent screen
• Lets her arrange the cover
• Place of refuge, crude forms of which can be found at the ends of 20- and 50-Across and 11- and 28-Down
• Protection from bad weather or danger
• Lieutenant in abrupt retreat
• Protected place
• Refuge, protection
• Officer shortly to penetrate clear harbour
• Haven