Dock 2 and 4 can't be used. Dock 1 brings you to the island Amaranthe and Dock 3 to Minsk Harbour in Dorgania. However, you can't access into MInsk Harbour until the main story is advanced far enough.
In order to take a ship, you need to buy tickets for all party members. So if you have 12 party members, you need 12 tickets. The tickets can be bought in the right port authority building in Havaria Port.
The temple island of Mira's events is not part of the normal docks. If the events of Maria and the ice spirit are far enough, they'll appear in the top left of Havaria Port, and you can talk with them to teleport to the temple island.