Ships Basic Usage
(written by Auratus; from Ubi Forums)

Ships.... a lot different from Settlers III. And buggy and never fixed. Various things about them:
1. The "escort" feature doesn't apparently work for warships.
2. Build a shipyard to make ships: Warship (needs ammo; make an ammo building when applicable to your race; Vikings use mana), Ferry (carry troops and specialists), and Transport Ship (carry goods automatically when conditions regarding harbours are correct, but "buggy").
3. Build a harbour to transport goods around between harbours via Transport Ships: Click a Harbour, click arrow symbol with "x" and set cursor arrow at another harbour desired to be the destination. Click harbour to send goods. Click arrow in circle (goods menu appears). Click goods category, click good and then click amount. Use infinite at your own risk of crashing the game. Set in exact amounts to be shipped to the other harbour. Now... if a Transport Ship is built, it will arrive and begin to wait for loading of the goods by Settlers. It'll leave to the other harbour when loaded. At the other harbour, the unloaded goods may not appear, but click the harbour and you'll see that the goods have been delivered.
4. Use ferries to move specialists (pioneers, prospectors, thieves) and soldiers around. Move the ferry next to land. Select unto 15 settlers and then click onto the ferry. If all went well, they will board. Certain ferries (i.e. Trojans) are fickle about where to be click-on in order to acknowledge your command.
5. Warship get ammo by being adjacent to a shipyard. Warships will attack towers and all other ship types not allied. The Viking warship needs huge amounts of mana, not normal ammo, in order to fire at an enemy.
6. Remember that enemy archers can attack ships parked too close to them.
7. A harbour land-locked in a pond or in-land sea will still receive shipments from other harbours via a "bug" some call the "telaport bug." Simply connect the harbours as described in step 3 above. Be sure a transport ship can arrive at the sending harbour to load up on goods. When full, it will "teleport" all of it's cargo to the otherwise impossible to reach harbour.
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8. Use ferries to carry thieves whom are carrying stone and wood. Send them to a new island for starting new settlement. You'll need to bring pioneers and prospectors and one soldier (for a tower). Pioneer the land some, then queue up a tower for construction, then tell the thieves to set their goods on the ground. Convert some thieves, pioneers, and prospectors into settlers. Tell some settlers to become builders and diggers. The tower will soon be under construction. Next, built a harbour or market place (these need mules with a direct land route to another source market place) in order to receive more supplies to the new settlement.