Trade routes are where you set a ship to automatically trade for you, it's good because you don't have to worry if you set it up right but you won't get a 5% boost on trading if you chose that boost to start off with.
Trade Map[edit]
The trade map will give you the choice of towns to trade with, a fully completed map is here, choose a few towns close to each other (preferably all with permits) and click on each of them once then click edit, you can make the captain trade the way he wants if you want but it is strongly recommended that you don't, instead, choose manual trading which is hidden away in the options and choose the goods that you want and the max and minimum price. Note that you will need to change get from warehouse to get from city by clicking the warehouse icon.
Repairing Ships[edit]
If you want, choose to repair in the town who is friendlier to you.
If you have your own town, heal there, it costs nothing.