I've played a few games now and used some of the tips on this thread as guidance. I always like to think of the different philosophies around game play. Here is one that I've found very useful and I hope this gives you a bit of a new perspective on game play :
First off this isn't Civ, so it's OK to build cities close to each other if they have enough resources to do your bidding.
The trade good colony
Have as many specialized workers on the field harvesting trade goods with farmers/fishermen to support your working men. That way you can have up to 6 squares for trade goods and 2 for food.
The port
The port city can manage with 6 squares because it doesn't have to harvest trade goods. It really only needs food. Just enough for your specialists who process the trade goods and to make more colonists. Build factories in this city to process the trade goods.
Necessities Colony
Build this colony close to ore and wood. Produce tools and guns here. Send wood and tools to the other two colonies when needed. This colony will make you more independent from Europe. Make this a port colony if you want to make ships.
Now that's the basics of the strategy, I wanna keep this as short as possible
You can add a 4th colony that could produce massive amounts of food to make colonists and horses perhaps. Or if one of your other 3 colonies are not up to there tasks.
The main thing is that you have an X amount of time to prepare for war. So you need to confine how many colonies you want to build and manage and how many will really help your goals of victory. It's not like in Civ where the more cities the better.
Good luck and have fun
P.S.
Don't automate the pioneers, they kinda chop down trees in the wood colony or build a cabin instead of a farm. Best to control them yourself to fit your priorities.