LOL, we all play the game in different way's so what works for one might not work for another, although that been said the way the trading works in COAs is it will work for all. So basically visit all ports under the nation you are playing as and all the friendly ports to that nation. Since pirates are not going to attack you in their ports its a good idea to visit them as well. In each port view the goods list in each town. I tend to do merchant runs for the store owner's till my trading skill is better (about 30% should be good enough). While doing the merchant runs i also look at the stores goods lists because that way they will show up in the trade tab. Now all i have to do is look who exports what and how much of that good they have and then who imports it and for how much. Generaly the more they have of any given good the less it costs. So the bigger the profit, Mahogany, Silver, Gold, Iron etc sell very well. But most of the time i will start off by selling Sadalwood because some stores tend to have so much of it that its easy money and its not that hard to make a profit from it.
Before your ready to start manually trading though, get yourself (if you haven't already) a good officers who has better trading skills then you do because that will help a lot. Try to get the trading perks asap because they are very important when playing as a merchant. When your trading skill is higher, get a trade license and visit all ports under that nations flag that you can before the license runs out. Don't forget you are only going their to find out what goods the store imports and exports, so visit the store and look at the goods lists. Now you are ready to compare the towns that export the high rolling goods. Gold, Silver, Mahogany, Ebeny, Sandalwood and don't forget Slaves. Now try to find the closest store that imports one the goods the other store exports. You might want to have a few trading ships like 2 to 3 Pinnace's, Galleon's, Fleuts etc for this. Don't bother arming your ships to the teath because the more room you use for ammo and weapons the less goods you can sell. More so if you have both realistic goods price and realistic goods weights turned on. Also note that the higher the calibure you have mounted the more cargo space they take up, aspecialy if they are culverines. Get a trade license for the port that imports those goods (if needed) and start transporting the goods to it. You will soon be rolling in money.
For this i tend to have a Corvette, Frigate or some other fast but well armoured ship as my flag ship and the trade ships under the AI captains control. This way i can defend the convoy and be able to get in to help any one of my Ai captains out if they need it. Remember you don't need to sink the enemy to escape. Knipple shot will do just fine, take their sail hp down and you will have very little trouble from them. This helps against large enemy convoy's who out number you, because you slow them down enough to allow your trade ships to escape and then you turn and follwo them.
Hope these tips help.