The fundamental rule of colony management - transfer all your colonists *only* on horseback. (unless you can go faster on ships, or they aren't going further than 3 squares, so the horses won't help any, but you already know that)
This way you can get the colonists you need - Elder Statesmen for improving sons of liberty membership, carpenters for building things, free colonists for education, graduates for work, pioneers for building roads, armies for defence etc. in just one turn.
You need roads, or at least rivers or plain terrain for that. You'll also need a lot of horses, warehouses and wagon trains (as the transport in one direction may be bigger than in the other, you may have to move the horses back).
That's a lot of infrastructure, but as you can transport colonists quickly, you won't waste precious labor and you can very quickly get everyone to work in the skill he's good at (no more experts wasting their skills just because they're in a wrong place). As the local labor allocation will be close to optimal for given workforce, you will be able to get or train colonists with necessary skills to improve global labor allocation too.
Good colony management is going to double your efficiency.
Don't bother with producing everything in the place where it's consumed (food, lumber, ore). You can transport a lot quickly if only you have roads, warehouses and wagon trains.
In the mid game set your aim at producing as much lumber and tools per turn as you can, and turning all that into buildings (the most important ones are: lumber mill, warehouse, printing presses, docks, newspaper, warehouse expansion, stable) and roads. Plowing, clearing forests, making guns, stockades and cash factories are a secondary but also important task.
Get Master Carpenters (on horseback) into each new colony to build the lumber mill and warehouse as soon as possible, with imported food and lumber. Then maybe make a printing press and get some Elder Statesmen to work there. You should make it your priority for at all your colonies to operate at +1 bonus (50%-99% sons of liberty), +2 bonus (100%) is nice, but may be too costly. You start with 20% support after Bolivar, so you can get three colonies +1 in the time it takes to get one colony +2. Remove all unnecessary colonists (horseback of course) if they interfere with that goal.
Because you need a lot of Master Carpenters and Elder Statesmen, train as many colonists as you can in those skills. You need an University for the latter, so you will have to use untrained statesmen until relatively late game, but the Carpenters are cheap and need only a Schoolhouse, so get them fast.