I have only played Patrician 3, so take my experience with a grain of salt.
In my experience auto trading as plain trading is just a money hole. What you want to do is set up trade offices in multiple cities, produce a set of your own goods (beer, iron goods, wine and meat are profitable), and use auto routes to distribute goods among your offices. Then you just set acceptable sale prices in those. You'll need to fine tune the whole system now and then by adding more ships to convoys, changing sale prices, building additional production facilities etc, but overall it's a bit more manageable than using routes for buying goods from towns, and it's a lot more profitable.
I only played Port Royale 2, and not a single Patrician game, so take my experience with even more salt:
What I did was to create one convoy which gets all the goods you produce from all over the gameworld and brings it to a central hub city. If you want/need to, you can make that convoy transport resources needed for production, as well.
Then, in the central hub, load up a different convoy with all the stuff you produced, and set it to autotrade with the cities you desire.
That way, you don't need to adjust prices in the offices. If the trading captain AI is smart enough, that is.
If done right (and if the game allows it), all you need to do is add ships once in a while. (Since convoy size is probably limited, that means new convoys, too, once in a while, but you can just copy ye olde ones.) Oh, and you need to add production facilites from time to time, too, of course.