Yes, technically if you are at the market you cannot see the harbour as it is underneath you, (think huge caverns with an entrance which was the tunnel we sailed into to get to the Harbour which lies in a huge Caverns and hidden away and in order to get to the city you have to climb the stairs up to groundlevel into the market.

As the skies are literally floating landmasses/islands imagine a multilayered type of City with a huge excavated underground harbour.