At the governor you can plead for an audience, where he will tell you if your reputation is increasing or decreasing with that nation. This will also update your reputations points on the Diplomacy screen.
You can also look at the Industry information. This includes supply and demand, and what types of factories the town has for production. This can be useful to see if a town will produce wood and cloth while you stay there.
The last option is to join the nation of that city. You need +500,000 diplomacy points with a nation to be able to join it.
City Management: If you capture a city you won't see the normal governor options but will be presented with the city management screen. This allows to check your wealth and your citizens status. It will also allow you to send money to the town and hire soldiers for defense.
In the information center of the city you will receive important details about the city status. You can see several events on the news board like fights near the city or lack of goods.
You can accept several tasks from the "Jobs" board to earn money or reputation points for the respective nation.
You can also check the Diplomacy of the city's nation and who they are at war with.
At the merchant screen you can buy and sell goods. The prices of the goods on the merchant screen depend on the city stocks. The more stocks there is the less they will pay. Keep in mind that if you don't have enough fishers or cooks, you should always buy enough food or rum for your crew otherwise they will mutiny and cause you to lose a ship if not more.
In the pub you have the possibility to hire crew. Ship boys are always present but better crew like seamen or veterans have to be lured into the pub by paying for a round of rum. Additionally you can increase the morale of your own crew by buying rum for them.
Specialists: From time to time there are specialists present in the pub who have great abilities. A navigator increases the speed of your fleet or allows you to use more ships at the same time, a look-out man increases the visibility range of your fleet for a faster identification of enemy ships.
You have to pay a continuous amount of gold for the specialists. But if a specialist stays with you a certain amount of time, he/she will become loyal and won't leave you when rafted, however they will leave if you can't pay them.
A detailed list of specialists is available in Specialists.
Sometimes you will meet other people who offer you information. This will not happen often but you will receive a message if someone wants to offer you something.
Bounties: Bounties can be set on other human players for a minimum of twenty thousand gold, these can be set to sink a ship above a minimum class. If a bounty was set on a player you will see a little coin behind his name when you meet the player on sea. Also bounties will be added automatically when a nations city is captured by another nation. For reclaiming the city you will receive thirty thousand gold.
If you don't want to lose your hard earned gold to the sea or pirates you should deposit it in the bank. Your gold is safe in the bank. But above a certain amount of gold you have to pay taxes. Also, note that not all cities have banks. Your money will be available in only cities that have a bank.
In the ship yard you can order new ships to be built, sell or buy used ships and upgrade or repair your fleet. Please notice, that not every yard can take every ship. Smaller yards usually have no space for larger ships. The yard will also work on your orders if you are offline because the time in the world doesn't stop. A detailed list of all ship types can be found in Ship Classes. Additionally you can buy and sell cannons and ammunition in the yard.
In the harbour you can moor your ships, by doing so you have to pay anchor fee, the more ships you moor the higher the fee gets. Ships condition in harbour will over some time decay to 10%. You can only moor roughly 11 times your Nav in ship cost.
In the harbour you can also take a transit. Here you have to sell all your goods, weapons and moor your ships, then its possible to hire a NPC to sail you to another port.
Note: Do NOT take a transit if you have any unloyal specialists, otherwise you will lose all unloyal specialists.